All of this material will appear on the exam. Take notes on the workflow, functions, and concepts.
By the end of this lesson you will know how to..
getwd()list.files(pattern = ...)read.csv()dim(), summary(), etc.)This Portfolio is a complete worked example of a PCA analysis of a dataset. It covers all relevant issues
This Portfolio also expands on our understanding of PCA by introducing the concept of PCs explain a proportion of the variation of the data. This is useful for understanding what PC does and what the PCs mean, and also allow us to interpret screeplots more thoroughly.
Check the location of your working directory with
getwd()
# run getwd()
setwd("C:/Users/mikaw/OneDrive/Pitt/Computational Biology/my_snps")
getwd()## [1] "C:/Users/mikaw/OneDrive/Pitt/Computational Biology/my_snps" # TODOCheck for the presence of the “walsh2017morphology.csv” file in the
working directory with list.files()
list.files()## [1] "(Studies in Feminist Philosophy) Elizabeth Brake - Minimizing Marriage_ Marriage, Morality, and the Law-Oxford University Press (2012).pdf"
## [2] "0110 F20 Recitation Worksheet 2 Key Updated to Post September 10.pdf"
## [3] "0110 F20 Recitation Worksheet 2 Send (1).pdf"
## [4] "0110 F20 Recitation Worksheet 2 Send.pdf"
## [5] "0110 F20 420 PM Syllabus Updated with Canvas Compliance (1).pdf"
## [6] "0110 F20 420 PM Syllabus Updated with Canvas Compliance.pdf"
## [7] "0110 F20 Lab 8 Thermochemistry I Updated for Openstax (1).pdf"
## [8] "0110 F20 Lab 8 Thermochemistry I Updated for Openstax (2).pdf"
## [9] "0110 F20 Lab 8 Thermochemistry I Updated for Openstax.pdf"
## [10] "0110 F20 Outline of Possible Final Exam Material.pdf"
## [11] "0110 F20 Recitation Skills Inventory for Students Send (1).pdf"
## [12] "0110 F20 Recitation Skills Inventory for Students Send.pdf"
## [13] "0110 F20 Recitation Skills Inventory Worksheet Key Send (1).pdf"
## [14] "0110 F20 Recitation Skills Inventory Worksheet Key Send.pdf"
## [15] "0110 F20 Recitation Worksheet 1 For Students (1).pdf"
## [16] "0110 F20 Recitation Worksheet 1 For Students.pdf"
## [17] "0110 F20 Recitation Worksheet 2 Key Send (1).pdf"
## [18] "0110 F20 Recitation Worksheet 2 Key Send.pdf"
## [19] "0110 F20 Schedule Post.pdf"
## [20] "0110 F20 Schedule Updated Post (1).pdf"
## [21] "0110 F20 Schedule Updated Post (2).pdf"
## [22] "0110 F20 Schedule Updated Post (3).pdf"
## [23] "0110 F20 Schedule Updated Post (4).pdf"
## [24] "0110 F20 Schedule Updated Post.pdf"
## [25] "0110 F20 Worksheet for Recitation Week beginning November 12.pdf"
## [26] "0110 FP20 OpenStax Chapter 4 Notes for Students to Use.pdf"
## [27] "020_W12D1_TWA Voc List UNIT 3.2 Relationships (Cohort).docx.rtf"
## [28] "020_W12D2_TWA UNIT UNIT 3.4 (Modal Verbs & Classifiers).pptx.pdf"
## [29] "07-mean_imputation.docx"
## [30] "07-mean_imputation.html"
## [31] "07-mean_imputation.Rmd"
## [32] "08-PCA_worked.Rmd"
## [33] "1.10D-618F (1).ab1"
## [34] "1.10D-618F.ab1"
## [35] "1.11B-618F (1).ab1"
## [36] "1.11B-618F.ab1"
## [37] "1.11F-618F (1).ab1"
## [38] "1.11F-618F.ab1"
## [39] "1.11G-618F.seq"
## [40] "1.12G-618F.ab1"
## [41] "1.12G-618F.seq"
## [42] "1.12G-619R (1).ab1"
## [43] "1.12G-619R.ab1"
## [44] "1.12H-618F.seq"
## [45] "1.12H-618F_R (1).ab1"
## [46] "1.12H-618F_R.ab1"
## [47] "1.12H-618F_R.seq"
## [48] "1.12H-619R (1).ab1"
## [49] "1.12H-619R (2).ab1"
## [50] "1.12H-619R.ab1"
## [51] "1.3 worksheet.pdf"
## [52] "1_brkS1_3RenRDNRS.ab1"
## [53] "10_11 Class Notes.docx"
## [54] "102622 lg.pdf"
## [55] "102822 lg.pdf"
## [56] "110422 lg.pdf"
## [57] "110722 lg (1).pdf"
## [58] "110722 lg.pdf"
## [59] "110922 lg.pdf"
## [60] "111122 lg (1).pdf"
## [61] "111122 lg.pdf"
## [62] "111422 lg.pdf"
## [63] "112822 lg.pdf"
## [64] "1530 Syllabus 2021-22.docx"
## [65] "1540_in_class_exercise_random_numrbers.pdf"
## [66] "1D-616F.ab1"
## [67] "2.2 workbook 11-2016.pdf"
## [68] "2.2E-618F.seq"
## [69] "2.2E-618F_R (1).ab1"
## [70] "2.2E-618F_R.ab1"
## [71] "2.2E-618F_R.seq"
## [72] "2.2E-619R (1).ab1"
## [73] "2.2E-619R.ab1"
## [74] "2015KEY (1).pdf"
## [75] "2015KEY.pdf"
## [76] "2019_12_04 Hainer Lab meeting.pptx"
## [77] "2020 Cailin Jordan Horowitz Fellowship Final Report.docx"
## [78] "2020 Horowitz family letter.docx"
## [79] "2020 Horowitz Fellowship Research Statement (1).docx"
## [80] "2020 Horowitz Fellowship Research Statement.docx"
## [81] "2021Movie#1.docx (1).pdf"
## [82] "2021Movie#1.docx.pdf"
## [83] "2022 Mika Wesley Horowitz Research Report.docx"
## [84] "2022 Summer Fellowship application .docx"
## [85] "2022 Summer fellowship instructions (1).docx"
## [86] "2022 Summer fellowship instructions (2).docx"
## [87] "2022 Summer fellowship instructions (3).docx"
## [88] "2022 Summer fellowship instructions.docx"
## [89] "210702 big Lab meeting projects12 (1).pptx"
## [90] "210702 big Lab meeting projects12.pptx"
## [91] "220316 D1R PCR screen A7-12 B7-12(1).tiff"
## [92] "220316 D1R PCR screen A7-12 B7-12.TIF"
## [93] "220316 D1R PCR screen A7-12 B7-12.tiff"
## [94] "220317 D1R digest screen A7-12 B7-12(1).tiff"
## [95] "220317 D1R digest screen A7-12 B7-12.TIF"
## [96] "220324 PCR test BB RS gDNA temp(1).tiff"
## [97] "220325 another test MW plate diluted and sarahs plate(1).tiff"
## [98] "220328 braulio test MW primers w MWgDNA SHgDNA A1 SH primers w MW gDNA SHgDNA A1(1).tiff"
## [99] "220331 D1R candidates A1 A2 B3 A4(1).tiff"
## [100] "220331 D1R candidates A1 A2 B3 A4.TIF"
## [101] "220407 D1R digest A1 A2 B3 A4.tiff"
## [102] "220414 D1R PCR screen A1_A2_B3_A5_B2_B5_B6_A5.tiff"
## [103] "220418 D1R row 5 and 5BC RD_ PCR A1_A2_B3_A4_B2_B5_B6_A5 2.tiff"
## [104] "220418 D1R row 5 and 5BC RD_ PCR A1_A2_B3_A4_B2_B5_B6_A5.tiff"
## [105] "220421 RA3 (conc 20_80_200) and B3 (conc 20_80_200).tiff"
## [106] "220422 PCR new primers row 2_ A1_ B3_ A4.tiff"
## [107] "220426 PCR test B3(133 at 60 and 65_ 616 at 60 and 65) other DNA(113 at 60 and 65_ 616 at 60 and 65).tiff"
## [108] "220428 PCR row2 (4 and 8ul).tiff"
## [109] "220428 PCR test 60_ 65_ 70 B3_ A1 different primers.tiff"
## [110] "220429 PCR row3 (4 and 8ul) (1).tiff"
## [111] "220429 PCR row3 (4 and 8ul).tiff"
## [112] "220429 PCR test 60_ 65_ 70 B3_ A4 different primers.tiff"
## [113] "220509 PCR row 4 (primers 113_ 109_ 115).tiff"
## [114] "220510 PCR 60 degrees A4 primers 113_ 109_ 115.tiff"
## [115] "220510 PCR 65 degrees A4 primers 113_ 109_ 115.tiff"
## [116] "220511 PCR A4 primer 113 (57_ 60_ 63)_ A4 primer 109 (60).tiff"
## [117] "220511 PCR A4 primers 113_114.tiff"
## [118] "220512 PCR wt gDNA primers 113_114.tiff"
## [119] "220513 PCR primers 113.114"
## [120] "220516 PCR 616_114 and 109_110 row 10 wt (1).tiff"
## [121] "220516 PCR 616_114 and 109_110 row 10 wt.tiff"
## [122] "220517 PCR row 7 wt 616_114 and 109_110 6 ul.tiff"
## [123] "220517 PCR targetted BC plate row 10 616_114.tiff"
## [124] "220517 PCR wt row 7 616_114 and 109_110 8 ul.tiff"
## [125] "220518 PCR wt gDNA primers 618_619 and 109_110.tiff"
## [126] "220520 PCR wt row 8 primers 618_619.tiff"
## [127] "221013 D3L, D2L, PxL.SQV"
## [128] "221018 D2L, PxL, and D3R row 1 RD.TIF"
## [129] "221110 D3R Rd rows 7 to 12 (pxL positive control at end).TIF"
## [130] "2C-616F_R.ab1"
## [131] "2C-616F_R_R.ab1"
## [132] "2E-616F_R.ab1"
## [133] "2E-616F_R_R.ab1"
## [134] "2H-616F_R.ab1"
## [135] "2H-616F_R_R.ab1"
## [136] "3B-616F_R.ab1"
## [137] "3B-616F_R_R.ab1"
## [138] "3E-616F_R.ab1"
## [139] "4G-616F_R.ab1"
## [140] "4G-616F_R_R.ab1"
## [141] "4sU Labelling and Labelled RNA Isolation (1).docx"
## [142] "4sU Labelling and Labelled RNA Isolation.docx"
## [143] "5A-616F_R.ab1"
## [144] "5A-616F_R_R.ab1"
## [145] "5B-616F_R.ab1"
## [146] "5B-616F_R_R.ab1"
## [147] "6C-616F_R.ab1"
## [148] "6C-616F_R_R.ab1"
## [149] "6F-616F_R.ab1"
## [150] "6F-616F_R_R.ab1"
## [151] "6H-616F_R.ab1"
## [152] "6H-616F_R_R.ab1"
## [153] "A_Companion_to_Contemporary_French_Cinema_----_(2_“Do_We_Have_the_Right_to_Exist_”_French_Cinema_Culture_and_World_Tra...).pdf"
## [154] "A3-111F.ab1"
## [155] "A3-111F_R.ab1"
## [156] "Abortion Resources.pdf"
## [157] "About you (1).docx"
## [158] "About you.docx"
## [159] "ABR Module 1 PowerPoint.pdf"
## [160] "Abstract (1) (1).docx"
## [161] "Abstract (1).docx"
## [162] "Abstract.docx"
## [163] "Academic Transcript.pdf"
## [164] "Acquire(1).pkg"
## [165] "Acquire.pkg"
## [166] "Activity 9_ Electrophilic Aromatic Substitution Reactions_ Bromination of Aniline and N-Acetylaniline (1).pdf"
## [167] "Activity 9_ Electrophilic Aromatic Substitution Reactions_ Bromination of Aniline and N-Acetylaniline.pdf"
## [168] "actual expression clone.ape"
## [169] "Additional Questions.docx"
## [170] "Additional Questions_SH (1).docx"
## [171] "Additional Questions_SH.docx"
## [172] "Adjectives (1).docx"
## [173] "Adjectives.docx"
## [174] "Adli_2018_CRISPRreview.pdf"
## [175] "aligned to SB.png"
## [176] "aligned to WT.png"
## [177] "ALL.chr6_GRCh38.genotypes.20170504 (1).vcf.gz"
## [178] "allomtery_3_scatterplot3d (1).Rmd"
## [179] "An_effect_of_DNA_sequence_on_nucleosome_occupancy_ (1).pdf"
## [180] "An_effect_of_DNA_sequence_on_nucleosome_occupancy_.pdf"
## [181] "Analysis of classmates data interpretation.docx"
## [182] "Anne Fausto-Sterling, “Dueling Dualisms” .pdf"
## [183] "annotated-Journal%202.docx.pdf"
## [184] "annotated-Reflection%20Paper%201.docx.pdf"
## [185] "annotated-Response%20Paper%202%20%281%29.docx.pdf"
## [186] "annotated-Sequence%20Analysis%202.docx.pdf"
## [187] "Annotated Bibliography.docx"
## [188] "Antigone FR0221.pptx"
## [189] "Ape_program.docx"
## [190] "ApE_win_current.zip"
## [191] "APP1210_New_Application_From_Ericka_9.24.20 (1).pdf"
## [192] "APP1210_New_Application_From_Ericka_9.24.20 (2).pdf"
## [193] "APP1210_New_Application_From_Ericka_9.24.20.pdf"
## [194] "ar_biochem89_213.ris"
## [195] "ASL Stories (1).docx"
## [196] "ASL Stories.docx"
## [197] "Assignment 1 (Kofron et al.) - answer key.docx"
## [198] "ATPyS data raw (1).xlsx"
## [199] "ATPyS data raw (2).xlsx"
## [200] "ATPyS data raw.xlsx"
## [201] "ATT00001.txt"
## [202] "b02665c6ce0308c519bc5ca8cbbd02f0 (1).torrent"
## [203] "b02665c6ce0308c519bc5ca8cbbd02f0 (2).torrent"
## [204] "b02665c6ce0308c519bc5ca8cbbd02f0 (3).torrent"
## [205] "b02665c6ce0308c519bc5ca8cbbd02f0 (4).torrent"
## [206] "b02665c6ce0308c519bc5ca8cbbd02f0.torrent"
## [207] "bell hooks - All about Love_ New Visions-William Morrow Paperbacks (2001).pdf"
## [208] "Bey-Rozet_FR16_History_of_French_Cinema_Syllabus (1).docx"
## [209] "Bey-Rozet_FR16_History_of_French_Cinema_Syllabus (2).docx"
## [210] "Bey-Rozet_FR16_History_of_French_Cinema_Syllabus (3).docx"
## [211] "Bey-Rozet_FR16_History_of_French_Cinema_Syllabus (4).docx"
## [212] "Bey-Rozet_FR16_History_of_French_Cinema_Syllabus (5).docx"
## [213] "Bey-Rozet_FR16_History_of_French_Cinema_Syllabus (6).docx"
## [214] "Bey-Rozet_FR16_History_of_French_Cinema_Syllabus (7).docx"
## [215] "Bey-Rozet_FR16_History_of_French_Cinema_Syllabus (8).docx"
## [216] "Bey-Rozet_FR16_History_of_French_Cinema_Syllabus (9).docx"
## [217] "Bey-Rozet_FR16_History_of_French_Cinema_Syllabus.docx"
## [218] "Binder3-was s21 doc cam intro imf.pdf"
## [219] "BIo-Rad_EZ_Imager.docx"
## [220] "Bio ATP synthase + Fermmentation.pdf"
## [221] "BIOSC 0370 Syllabus, 2214.pdf"
## [222] "bird_snps_remove_NAs.html"
## [223] "bird_snps_remove_NAs.Rmd"
## [224] "Book Report (1).docx"
## [225] "Book Report.docx"
## [226] "BookLot.17.2102.1pawk (1).exe"
## [227] "BookLot.17.2102.1pawk.exe"
## [228] "BookScanCenter (1).pdf"
## [229] "BookScanCenter (2).pdf"
## [230] "BookScanCenter.pdf"
## [231] "Bottom Flowers and Placement.jpeg"
## [232] "Britt Wray, Generation Dread- Finding Purpose in an Age of Climate Change, Chapters 1 & 9.pdf"
## [233] "brk_coding_region (1).ape"
## [234] "brk_coding_region.ape"
## [235] "BS1520-Lecture 1.pptx"
## [236] "Buchsbaum - Do We Have a Right to Exist.pdf"
## [237] "c0110_expt1_intro.pdf"
## [238] "c0110_expt1_online.pdf"
## [239] "c0110_expt10 (1).pdf"
## [240] "c0110_expt10.pdf"
## [241] "c0110_expt11_intro.pdf"
## [242] "c0110_expt12_intro (1).pdf"
## [243] "c0110_expt12_intro.pdf"
## [244] "c0110_expt12_online_fillable_pdf.pdf"
## [245] "c0110_expt2_intro.pdf"
## [246] "c0110_expt2_online (1) (1).pdf"
## [247] "c0110_expt2_online (1) (2).pdf"
## [248] "c0110_expt2_online (1).pdf"
## [249] "c0110_expt3_intro (1).pdf"
## [250] "c0110_expt3_intro (2) (1).pdf"
## [251] "c0110_expt3_intro (2).pdf"
## [252] "c0110_expt3_intro (3).pdf"
## [253] "c0110_expt3_intro.pdf"
## [254] "c0110_expt3_online-1.pdf"
## [255] "c0110_expt3_online-2 (1).pdf"
## [256] "c0110_expt3_online-2.pdf"
## [257] "c0110_expt3_online.pdf"
## [258] "c0110_expt4_intro (1).pdf"
## [259] "c0110_expt4_intro (2).pdf"
## [260] "c0110_expt4_intro.pdf"
## [261] "c0110_expt4_online (1).pdf"
## [262] "c0110_expt4_online.pdf"
## [263] "c0110_expt5_intro (1).pdf"
## [264] "c0110_expt5_intro (2).pdf"
## [265] "c0110_expt5_intro.pdf"
## [266] "c0110_expt6_intro (1).pdf"
## [267] "c0110_expt6_intro (2).pdf"
## [268] "c0110_expt6_intro.pdf"
## [269] "c0110_expt7Iintro.pdf"
## [270] "c0110_expt8_intro (1).pdf"
## [271] "c0110_expt8_intro.pdf"
## [272] "c0110_expt9_intro (1).pdf"
## [273] "c0110_expt9_intro (2).pdf"
## [274] "c0110_expt9_intro (3).pdf"
## [275] "c0110_expt9_intro (4).pdf"
## [276] "c0110_expt9_intro (5).pdf"
## [277] "c0110_expt9_intro.pdf"
## [278] "c0120_expt1_online_fillable-merged (1).pdf"
## [279] "c0120_expt1_online_fillable-merged (2).pdf"
## [280] "c0120_expt1_online_fillable-merged.pdf"
## [281] "c0120_expt10.pdf"
## [282] "c0120_expt11_intro.pdf"
## [283] "c0120_expt11_online_fillable_PDF.pdf"
## [284] "c0120_expt12_online_fillable-merged.pdf"
## [285] "c0120_expt12_online_fillable.pdf"
## [286] "c0120_expt2_chromatograms (1).pdf"
## [287] "c0120_expt2_chromatograms.pdf"
## [288] "c0120_expt2_intro (1).pdf"
## [289] "c0120_expt2_intro.pdf"
## [290] "c0120_expt2_online.fillable (1).pdf"
## [291] "c0120_expt2_online.fillable.pdf"
## [292] "c0120_expt3_intro.pdf"
## [293] "c0120_expt3_online_fillable-1.pdf"
## [294] "c0120_expt3_online_fillable.pdf"
## [295] "c0120_expt4_intro.pdf"
## [296] "c0120_expt4_spectra.pdf"
## [297] "c0120_expt4_spectra.xlsx"
## [298] "c0120_expt5 (1).pdf"
## [299] "c0120_expt5.pdf"
## [300] "c0120_expt5_spectra2.xlsx"
## [301] "c0120_expt6_intro (1).pdf"
## [302] "c0120_expt6_intro.pdf"
## [303] "c0120_expt7_intro.pdf"
## [304] "c0120_expt8_intro.pdf"
## [305] "c0120_expt9_intro.pdf"
## [306] "Cahier d'activités.docx"
## [307] "calendar (1).ics"
## [308] "calendar.ics"
## [309] "cdc_83237_DS1.pdf"
## [310] "Cell&Dev_NEW GenEds_8.21.pdf"
## [311] "center_function (1).R"
## [312] "center_function.R"
## [313] "Certificate (3).pdf"
## [314] "Césars _ «Désormais on se lève et on se barre», par Virginie Despentes - Libération (1).pdf"
## [315] "Césars _ «Désormais on se lève et on se barre», par Virginie Despentes - Libération (2).pdf"
## [316] "Césars _ «Désormais on se lève et on se barre», par Virginie Despentes - Libération.pdf"
## [317] "Ch 7 Activities (1).docx"
## [318] "Ch 7 Activities.docx"
## [319] "Ch 8 Activities (1).docx"
## [320] "Ch 8 Activities.docx"
## [321] "Ch6 Activites (1).docx"
## [322] "Ch6 Activites.docx"
## [323] "Chan (1).pdf"
## [324] "Chan.pdf"
## [325] "chancellor's fellowship post 1 (Hainer, Sarah Jane).docx"
## [326] "chancellor's fellowship post 1.docx"
## [327] "chancellor fellowship post 2 (1).docx"
## [328] "chancellor fellowship post 2.docx"
## [329] "chancellor fellowship post 2_SH.docx"
## [330] "Chancellors Fellowship Research Proposal.docx"
## [331] "Chancellors Fellowship Research Proposal_SH.docx"
## [332] "Chancellors Fellowship Research Proposal2_SH (1).docx"
## [333] "Chancellors Fellowship Research Proposal2_SH (2).docx"
## [334] "Chancellors Fellowship Research Proposal2_SH.docx"
## [335] "chancellors post 3.docx"
## [336] "Chapitre 5 Workbook.pdf"
## [337] "Chapter 1 Structure and Bonding in Organic Molecules (1).docx"
## [338] "Chapter 1 Structure and Bonding in Organic Molecules answer key.docx"
## [339] "Chapter 1 Structure and Bonding in Organic Molecules.docx"
## [340] "Chapter 22_Lecture 24+25+26.pptx"
## [341] "Chapter 24_Lecture 30+31+32.pptx"
## [342] "Chapter I.pdf"
## [343] "Charles Rotation 2 Presentation_SH.pptx"
## [344] "Chem 310 Fall-2221 MSWORD.docx"
## [345] "Chem 310 FINAL EXAM-2211 (1) (1).doc"
## [346] "Chem 310 FINAL EXAM-2211 (1).doc"
## [347] "Chem 310 FINAL EXAM-2211 (2).doc"
## [348] "Chem 310 FINAL EXAM-2211.doc"
## [349] "Chem 310 Recitation Problem Set I-2211 (002).docx"
## [350] "ChemDraw Product User Guide (1).zip"
## [351] "ChemDraw Product User Guide (2).zip"
## [352] "ChemDraw Product User Guide (3).zip"
## [353] "ChemDraw Product User Guide.zip"
## [354] "ChemDraw QUICK START Activation Guide.pdf"
## [355] "Chemistry lab (1).pdf"
## [356] "Chemistry lab (2).pdf"
## [357] "Chemistry lab.pdf"
## [358] "Chromatography (Slides) (1).pdf"
## [359] "Chromatography (Slides).pdf"
## [360] "ChromeSetup.exe"
## [361] "ci_coding_region (1).ape"
## [362] "ci_coding_region.ape"
## [363] "class accession numbers 102022 (1).xlsx"
## [364] "class accession numbers 102022.xlsx"
## [365] "cluster_analysis_portfolio.Rmd"
## [366] "cluster_analysis_with_Higgs_aa.R"
## [367] "CODE_CHECKPOINT-first_rstudio_script (1).R"
## [368] "CODE_CHECKPOINT-first_rstudio_script (2).R"
## [369] "CODE_CHECKPOINT-first_rstudio_script.R"
## [370] "code_checkpoint_vcfR.html"
## [371] "code_checkpoint_vcfR.Rmd"
## [372] "codontable.pdf"
## [373] "Community Statement SURA_SH.docx"
## [374] "Community Statement_SH (1).docx"
## [375] "Community Statement_SH.docx"
## [376] "Composition 1 (1).docx"
## [377] "Composition 1.docx"
## [378] "Composition 2 (1).docx"
## [379] "Composition 2 .docx"
## [380] "Concept Map Kareem Wali FAR.pdf"
## [381] "Control_transgenes_sal_omb_HA_w_labels.jpg"
## [382] "ControversesCh7L5.pptx"
## [383] "ControversesCh7L8.pptx"
## [384] "Copy of recitation_13_student_vs - graph_paper_for_printing_or_tablet (1).pdf"
## [385] "Copy of recitation_13_student_vs - graph_paper_for_printing_or_tablet.pdf"
## [386] "Corrigé Ch 6-8.pdf"
## [387] "cos20.0 (1).exe"
## [388] "cos20.0 (2).exe"
## [389] "cos20.0.exe"
## [390] "Cover Letter.docx"
## [391] "Covid Vaccination.HEIC"
## [392] "Crimp, Accommodating Magic .pdf"
## [393] "CRISPR cas9.png"
## [394] "Critique Essay (1).docx"
## [395] "critique essay (1).pdf"
## [396] "Critique Essay (2).docx"
## [397] "Critique Essay (3) (1).docx"
## [398] "Critique Essay (3).docx"
## [399] "Critique Essay (4).docx"
## [400] "Critique Essay.docx"
## [401] "critique essay.pdf"
## [402] "Culture Analysis Essay (1).docx"
## [403] "Culture Analysis Essay.docx"
## [404] "customers_sampledataforleap.csv"
## [405] "CW001_CLR_ENG_24_41496023_1 (1) (1).PDF"
## [406] "CW001_CLR_ENG_24_41496023_1 (1).PDF"
## [407] "CW001_CLR_ENG_24_44450389_1.PDF"
## [408] "D11-112R.ab1"
## [409] "D11-112R_R.ab1"
## [410] "D1L_graphs.pzfx"
## [411] "D3R_gRNA-U6 (1).ab1"
## [412] "D3R_gRNA-U6.ab1"
## [413] "D3R_HC-M13F (1).ab1"
## [414] "D3R_HC-M13F (2).ab1"
## [415] "D3R_HC-M13F.ab1"
## [416] "DB5D1231-8A6E-464B-9ABC-7A74C803A998.jpeg"
## [417] "desktop.ini"
## [418] "Dev Bio UTA Review Packet – Exam 4.docx"
## [419] "Devoir 1 (1).docx"
## [420] "Devoir 1.docx"
## [421] "Devoir 2 (1).docx"
## [422] "Devoir 2 (2).docx"
## [423] "Devoir 2.docx"
## [424] "df (1).csv"
## [425] "df.csv"
## [426] "DiscordSetup.exe"
## [427] "Dissecting_and_fixing_wing_imaginal_discs.docx"
## [428] "Dissecting_and_fixing_wing_imaginal_discs_V1.1_3-23-22 (1).docx"
## [429] "Dissecting_and_fixing_wing_imaginal_discs_V1.1_3-23-22.docx"
## [430] "Dissecting_microscope.docx"
## [431] "DNA_concentration_determination_updated_2-2-22.docx"
## [432] "DNA_plasmid_Midiprep.docx"
## [433] "DNA_sequencing (1).xlsx"
## [434] "DNA_sequencing (2).xlsx"
## [435] "DNA_sequencing.xlsx"
## [436] "Doudna CRISPR 2014.pdf"
## [437] "Doudna CRISPR review.pdf"
## [438] "download.png"
## [439] "DownloadManager-v1.7.0.exe"
## [440] "E-mail What Not to Write (1).pdf"
## [441] "E-mail What Not to Write (2).pdf"
## [442] "E-mail What Not to Write.pdf"
## [443] "E GFP from destination vector DNA (1).ape"
## [444] "E GFP from destination vector DNA.ape"
## [445] "E GFP protein sequence 2022.docx"
## [446] "EB_NIH_Biosketch.docx"
## [447] "EC 4 (1).docx"
## [448] "EC 4.docx"
## [449] "EC 5 (1).docx"
## [450] "EC 5.docx"
## [451] "Ec week 3.pdf"
## [452] "EC3.docx"
## [453] "Egalité et droits des femmes dans la sphère privée _ Vie publique (1).pdf"
## [454] "Egalité et droits des femmes dans la sphère privée _ Vie publique.pdf"
## [455] "Embryo_injection.docx"
## [456] "en_coding_region (1).ape"
## [457] "en_coding_region (10).ape"
## [458] "en_coding_region (2).ape"
## [459] "en_coding_region (3).ape"
## [460] "en_coding_region (4).ape"
## [461] "en_coding_region (5).ape"
## [462] "en_coding_region (6).ape"
## [463] "en_coding_region (7).ape"
## [464] "en_coding_region (8).ape"
## [465] "en_coding_region (9).ape"
## [466] "en_coding_region.ape"
## [467] "enhancer_promoter looping (1).png"
## [468] "enhancer_promoter looping (2).png"
## [469] "enhancer_promoter looping (3).png"
## [470] "enhancer_promoter looping.png"
## [471] "entretien d'embauche.pptx"
## [472] "essay 1.docx"
## [473] "eve_coding_region.ape"
## [474] "Exam 3 Study Guide.pdf"
## [475] "Exam 3_Key.pdf"
## [476] "EXAMEN BLANC Corrigé.docx"
## [477] "examen final fr 4 aut20 (1).mp3"
## [478] "EXAMEN ORAL-en ligne (1).docx"
## [479] "EXAMEN ORAL-en ligne.docx"
## [480] "experiement 9-1.pdf"
## [481] "experiement 9.pdf"
## [482] "Experiment 8-1.pdf"
## [483] "Experiment1 (1).pdf"
## [484] "Experiment1.pdf"
## [485] "Experiment6.pdf"
## [486] "experiment8.pdf"
## [487] "Experimental Design (1).png"
## [488] "Experimental Design (2).png"
## [489] "Experimental Design.png"
## [490] "expression clone.ape"
## [491] "ExpressionsUtiles_ExprimerLaCause (1).docx"
## [492] "ExpressionsUtiles_ExprimerLaCause (2).docx"
## [493] "ExpressionsUtiles_ExprimerLaCause.docx"
## [494] "F.ape"
## [495] "F2_ Foundations of Biology 2 (Brouwer FALL 2020) _ Top Hat.pdf"
## [496] "FA-R Statement of Interest Review Form Peer to Peer.docx"
## [497] "FA-R Syllabus Weds 115PM Pittman (1).docx"
## [498] "FA-R Syllabus Weds 115PM Pittman.docx"
## [499] "feature_engineering.Rmd"
## [500] "feature_engineering_intro_2_functions-part2 (1).Rmd"
## [501] "feature_engineering_intro_2_functions-part2.Rmd"
## [502] "Feminist_science_who_needs_it.pdf"
## [503] "Final Essay (1).docx"
## [504] "Final Essay.docx"
## [505] "Final Exam Practice 2 KEY.pdf"
## [506] "Final Gloss.docx"
## [507] "Final Lab Report 1st draft updated 2-9-22 (1).docx"
## [508] "Final Lab Report 1st draft updated 2-9-22.docx"
## [509] "Final Paper (1).docx"
## [510] "Final Paper.docx"
## [511] "Final Project (1).docx"
## [512] "Final Project.docx"
## [513] "Final_lab_report_2nd_draft_updated_3-30-22.docx"
## [514] "Final_lab_report_2nd_draft_updated_4-5-22_v1.1.docx"
## [515] "Final_lab_report_final_2022_updated_4-8-22 (1).docx"
## [516] "Final_lab_report_final_2022_updated_4-8-22.docx"
## [517] "Final_lab_report_Final_rubric.docx"
## [518] "Finding Out Ch3"
## [519] "Finding Out Chapter One .pdf"
## [520] "Fine Slip Wesley.pdf"
## [521] "Firefox Installer.exe"
## [522] "First day of class.pptx"
## [523] "Forensics Lecture 4-4-22 v2 (1).pptx"
## [524] "Forensics Lecture 4-4-22 v2.pptx"
## [525] "form.PDF"
## [526] "foward.ape"
## [527] "FR 0220 Syllabus.docx"
## [528] "FR0104ExamenSemestrielAut2020 (1).docx"
## [529] "FR0104ExamenSemestrielAut2020.docx"
## [530] "FR0104SyllabusAUT20DAHL (1).doc"
## [531] "FR0104SyllabusAUT20DAHL (2).doc"
## [532] "FR0104SyllabusAUT20DAHL.doc"
## [533] "FR4hebdomadaireAUT20 (1).docx"
## [534] "FR4hebdomadaireAUT20.docx"
## [535] "France et Etats-Unis - Deux conceptions de la liberte d'expression (1).docx"
## [536] "France et Etats-Unis - Deux conceptions de la liberte d'expression (2).docx"
## [537] "France et Etats-Unis - Deux conceptions de la liberte d'expression.docx"
## [538] "FREN 0104 Midterm - Fall 2020Final (1) (1).docx"
## [539] "FREN 0104 Midterm - Fall 2020Final (1).docx"
## [540] "FREN 0104 Midterm - Fall 2020Final.docx"
## [541] "FREN 0104 MidtermEXBLANC (1).docx"
## [542] "FREN 0104 MidtermEXBLANC (2).docx"
## [543] "FREN 0104 MidtermEXBLANC.docx"
## [544] "french oral exam.mp4"
## [545] "French shrug at Petraeus' adultery - CNN (1).pdf"
## [546] "French shrug at Petraeus' adultery - CNN (2).pdf"
## [547] "French shrug at Petraeus' adultery - CNN.pdf"
## [548] "FRIT Flipbook Spring.pptx"
## [549] "Fugene CRISPR SH.docx"
## [550] "fullsizeoutput_79b.jpeg"
## [551] "Gender and Science Updated Syllabus 01.2021.docx"
## [552] "Gene Annotation Presentation Instructions and Template (1).pptx"
## [553] "Gene Annotation Presentation Instructions and Template.pptx"
## [554] "GeneJet_Minipreps_updated_2-2-22 (1).docx"
## [555] "GeneJet_Minipreps_updated_2-2-22.docx"
## [556] "GeneJET_Plasmid_Miniprep_UG_Summary.pdf"
## [557] "general image enhancer_promoter_gene (1).png"
## [558] "general image enhancer_promoter_gene.png"
## [559] "General_Lab_Instructions (1).docx"
## [560] "General_Lab_Instructions.docx"
## [561] "gimp-2.10.30-setup.exe"
## [562] "Gimp_image_editing_program_v1.2 (1).docx"
## [563] "Gimp_image_editing_program_v1.2.docx"
## [564] "glassware_specs.pdf"
## [565] "GPA-CALCULATOR.xls"
## [566] "green11 10x group 1-2.jpg"
## [567] "green3 10x group 1-2.jpg"
## [568] "Group.JPG"
## [569] "Group2 (1).JPG"
## [570] "Group2.JPG"
## [571] "Group3.JPG"
## [572] "GSWS First Day Info Sheet.asd.docx"
## [573] "GSWS First Day Info Sheet.docx"
## [574] "H8-112R.ab1"
## [575] "H9-111F.ab1"
## [576] "Hainer lab meeting.pptx"
## [577] "HainerLabExpectations-2.pdf"
## [578] "HainerLabExpectations.docx"
## [579] "Harris et al.pdf"
## [580] "Hatfull Lab UG application_Summer2021.pdf"
## [581] "Hatfull Lab UG_app_summer2021.doc"
## [582] "Hewitt - Salubrious Scandals, Effective Provocations.pdf"
## [583] "hooks, bell - Feminist Theory_ From Margin to Center-Routledge (2015).pdf"
## [584] "hooks, bell, _Feminist Politics_.pdf"
## [585] "horowitz end of summer report.docx"
## [586] "horowitz end of summer report_SH (1).docx"
## [587] "horowitz end of summer report_SH.docx"
## [588] "Horowitz Presentation_SH.pptx"
## [589] "Ice breaker.docx"
## [590] "IDP_worksheet.docx"
## [591] "IDP_worksheet_description.docx"
## [592] "IGV_Win_2.13.2-installer.exe"
## [593] "IGV_Win_2.13.2-WithJava-installer.exe"
## [594] "ijerph-18-00963 (1).pdf"
## [595] "ijerph-18-00963.pdf"
## [596] "ilovepdf_merged.pdf"
## [597] "images.jfif"
## [598] "IMG-0926 (1).jpg"
## [599] "IMG-0926.jpg"
## [600] "IMG-1088 (1).jpg"
## [601] "IMG-1088.jpg"
## [602] "IMG_0838 (1).jpg"
## [603] "IMG_0838.jpg"
## [604] "IMG_0913.jpeg"
## [605] "IMG_0962 (1).jpg"
## [606] "IMG_0962.jpg"
## [607] "IMG_0963 (1).jpg"
## [608] "IMG_0963.jpg"
## [609] "IMG_1020 (1).jpg"
## [610] "IMG_1020.jpg"
## [611] "IMG_1106 (1).jpg"
## [612] "IMG_1106.jpg"
## [613] "IMG_1108.jpg"
## [614] "IMG_1109.jpg"
## [615] "IMG_20210625_231257 (1).jpg"
## [616] "IMG_20210625_231257.jpg"
## [617] "IMG_20210628_180827 (1).jpg"
## [618] "IMG_20210628_180827.jpg"
## [619] "IMG_20210718_170822_662.jpg"
## [620] "IMG_20210718_170822_666.jpg"
## [621] "IMG_20210719_132218_2.jpg"
## [622] "IMG_20210719_150142.jpg"
## [623] "IMG_20210728_120703.jpg"
## [624] "IMG_20210813_165140.jpg"
## [625] "imovie-windows.exe"
## [626] "in class problems lecture 6 and 7.pdf"
## [627] "Informative Speech Outline.docx"
## [628] "InstallPrism9.msi"
## [629] "International Internship - Summer Draft Syllabus.pdf"
## [630] "International Internship - Summer Draft Syllabus_0.pdf"
## [631] "Interro écrite II-1.docx"
## [632] "Interro écrite II.docx"
## [633] "Intro.docx"
## [634] "invoices_sampledataforleap.csv"
## [635] "Jasmine_Dioguardi_CV.pdf"
## [636] "JavaSetup8u341.exe"
## [637] "jdk-18_windows-x64_bin.exe"
## [638] "Journal 2 (1).docx"
## [639] "Journal 2 (2).docx"
## [640] "Journal 2.docx"
## [641] "Journal 3 (1).docx"
## [642] "Journal 3.docx"
## [643] "K. Peter C. Vollhardt - Organic Chemistry_ Structure and Function-W. H. Freeman (2018).pdf"
## [644] "KiffeTaRace1 (1).docx"
## [645] "KiffeTaRace1.docx"
## [646] "KindleForPC-installer-1.32.61109.exe"
## [647] "Klein_CV.docx"
## [648] "knit (1).docx"
## [649] "knit.docx"
## [650] "knit.Rmd"
## [651] "Koisenu Futari 1 (1).ass"
## [652] "Koisenu Futari 1 (2).ass"
## [653] "Koisenu Futari 1.ass"
## [654] "Kvon et al.pdf"
## [655] "L'association Ni putes ni soumises est sur le point de disparaître _ la fin d'une époque _ (1).pdf"
## [656] "L'association Ni putes ni soumises est sur le point de disparaître _ la fin d'une époque _.pdf"
## [657] "La liberté d'expression, un concept différent en France et aux Etats-Unis (1).pdf"
## [658] "La liberté d'expression, un concept différent en France et aux Etats-Unis (2).pdf"
## [659] "La liberté d'expression, un concept différent en France et aux Etats-Unis.pdf"
## [660] "La main - Maupassant - make up assignment.docx"
## [661] "La main.docx"
## [662] "La Princesse de Cleves BD Adieu (1).pdf"
## [663] "La Princesse de Cleves BD Adieu.pdf"
## [664] "La Princesse de Cleves BD Aveu.pdf"
## [665] "La Princesse de Cleves BD Conclusion (1).pdf"
## [666] "La Princesse de Cleves BD Conclusion.pdf"
## [667] "La Princesse de Cleves passages (1).pdf"
## [668] "La Princesse de Cleves passages (2).pdf"
## [669] "La Princesse de Cleves passages.pdf"
## [670] "Lab 10 2022.docx"
## [671] "Lab 11-12 2022 (1).docx"
## [672] "Lab 11-12 2022.docx"
## [673] "Lab 13 2022.docx"
## [674] "Lab 14 Protocol.docx"
## [675] "Lab 3 2022.docx"
## [676] "Lab 5 2022 2.docx"
## [677] "Lab 6 2022.docx"
## [678] "Lab 7.docx"
## [679] "Lab 8 2022.docx"
## [680] "lab 8 Group 1-3 jpeg.jpg"
## [681] "Lab 9 2022 (1).docx"
## [682] "Lab 9 2022.docx"
## [683] "Lab Math review 020722.pdf"
## [684] "Lab Meeting Presentation 8-1_SH (1).pptx"
## [685] "Lab Meeting Presentation 8-1_SH.pptx"
## [686] "Lab_1_lecture_2022.pptx"
## [687] "Lab_10_2022_updated_3-23-22 (1).docx"
## [688] "Lab_10_2022_updated_3-23-22 (2).docx"
## [689] "Lab_10_2022_updated_3-23-22.docx"
## [690] "Lab_11-12_2022.docx"
## [691] "Lab_13_2022 (1).docx"
## [692] "Lab_13_2022 (2).docx"
## [693] "Lab_13_2022 (3).docx"
## [694] "Lab_13_2022.docx"
## [695] "Lab_14_Protocol.docx"
## [696] "Lab_2_lecture_2022.pptx"
## [697] "Lab_3_2022_updated_1-25-22.docx"
## [698] "Lab_3_lecture_2022.pptx"
## [699] "Lab_4_2022 (1).docx"
## [700] "Lab_4_2022.docx"
## [701] "Lab_5_2022_2.docx"
## [702] "Lab_7_updated_2-22-22 (1).docx"
## [703] "Lab_7_updated_2-22-22.docx"
## [704] "Lab_8_2022_updated_3-1-2022.docx"
## [705] "Lab_9_2022 (1).docx"
## [706] "Lab_9_2022.docx"
## [707] "Lab_Meeting_Presentation_4-6.pptx"
## [708] "Lab_notebooks.docx"
## [709] "Lab_notebooks_Labs_10-14_Expectations_2022.docx"
## [710] "Lab_notebooks_Labs_2-4_Expectations_2022.docx"
## [711] "Lab_notebooks_Labs_5_6_8_9_Expectations_2022.docx"
## [712] "labsyllabus_0110_2211.pdf"
## [713] "labsyllabus_0120_2214.pdf"
## [714] "Lahr_Berman_2015_pre_recitation_reading_week4_LARP.pdf"
## [715] "larp.PNG"
## [716] "Le jeu des catégories.docx"
## [717] "Le nord (1).docx"
## [718] "Le nord.docx"
## [719] "Le socialisme - reve ou realite (1).docx"
## [720] "Le socialisme - reve ou realite (2).docx"
## [721] "Le socialisme - reve ou realite.docx"
## [722] "LEAP Analytics Institute Session 2.xlsx"
## [723] "LEAP_UFO_DATA.xlsx"
## [724] "Lecture- La figure du migrant.docx"
## [725] "Lecture Learning Objectives - Module 1.pdf"
## [726] "lectures 21-23-- Gene regulation.pptx"
## [727] "Leica Microsystems.zip"
## [728] "Leland Hartwell, Michael L. Goldberg, Janice Fischer, Leroy Hood - Genetics_ From Genes to Genomes-McGraw-Hill (2017).pdf"
## [729] "Les «gilets jaunes» se trompent_ la vie à Paris n'a rien d'un conte de fées _ Slate.fr.pdf"
## [730] "Les partis politiques et les elections (1).pdf"
## [731] "Les partis politiques et les elections (2).pdf"
## [732] "Les partis politiques et les elections.pdf"
## [733] "Ligations (1).xlsx"
## [734] "Ligations.docx"
## [735] "Ligations.xlsx"
## [736] "Ligations_updated_1-31-22.docx"
## [737] "List of suggested films (1).pdf"
## [738] "List of suggested films.pdf"
## [739] "LittératureMondeEnFrançais.docx"
## [740] "LockDownBrowser-2-0-7-09.exe"
## [741] "M Topics for Chapter 12-S21.docx"
## [742] "M Topics for Chapter 18-S21.docx"
## [743] "M Topics for Chapters 16-17-21-S21 (1).docx"
## [744] "M Topics for Chapters 16-17-21-S21.docx"
## [745] "M Topics for Exam 1-annotated-S21.docx"
## [746] "M Topics for Exam 1-updated -S21 (1).docx"
## [747] "M Topics for Exam 1-updated -S21.docx"
## [748] "Mandated Reporter Certificate.png"
## [749] "map (1).exe"
## [750] "map.exe"
## [751] "Meillere_et_al_2015_telomeres_abridged_annotated (1).pdf"
## [752] "Meillere_et_al_2015_telomeres_abridged_annotated.pdf"
## [753] "MestReNova-LITE-CDE-12.0.1-20212.msi"
## [754] "Micropipettors.docx"
## [755] "MID Scholar Web Brochure_FINAL VERSION 081020.docx"
## [756] "Midipreps.xlsx"
## [757] "Midterm Paper (1).docx"
## [758] "Midterm Paper (2).docx"
## [759] "Midterm Paper.docx"
## [760] "Midterm.docx"
## [761] "Mika Wesley CV_SH.docx"
## [762] "Mika Wesley Resume_SH (1).docx"
## [763] "Mika Wesley Resume_SH.docx"
## [764] "Mika.JPG"
## [765] "Minipreps (1).xlsx"
## [766] "Minipreps (2).xlsx"
## [767] "Minipreps.xlsx"
## [768] "minitab20.3.0.0.x64"
## [769] "minitab20.3.0.0.x64.zip"
## [770] "minitab20.3.0.0setup.x64.exe"
## [771] "Modèle français ou américain _ les conceptions de la laïcité en Europe _ Vie publique.fr (1).pdf"
## [772] "Modèle français ou américain _ les conceptions de la laïcité en Europe _ Vie publique.fr.pdf"
## [773] "Moi, Mustapha Kessous, journaliste au _Monde_ et victime du racisme.pdf"
## [774] "MovaviVideoEditorPlusSetupC (1).exe"
## [775] "MovaviVideoEditorPlusSetupC.exe"
## [776] "MS_program_timeline_and_checklist_2019.docx"
## [777] "MW PxR RD plate 2 2-7 (1).scn"
## [778] "MW PxR RD plate 2 2-7 (2).scn"
## [779] "MW PxR RD plate 2 2-7.scn"
## [780] "Nascent rtqPCR.png"
## [781] "NetFx64.exe"
## [782] "new pcr product3.ape"
## [783] "News Assignment (1).docx"
## [784] "News Assignment (2).docx"
## [785] "News Assignment.docx"
## [786] "Ni-putes-ni-soumises.docx"
## [787] "Nihilism_and_Politics_The_Constrained_Life_Chances.pdf"
## [788] "non-fellowship-biosketch-sample-2021.docx"
## [789] "OfficeSetup (1).exe"
## [790] "OfficeSetup (2).exe"
## [791] "OfficeSetup.exe"
## [792] "Oligo Database (1).xlsx"
## [793] "Oligo Database.xlsx"
## [794] "order form.pdf"
## [795] "Other Approaches (1).png"
## [796] "Other Approaches.png"
## [797] "Other Arcadia Statements.docx"
## [798] "Other.png"
## [799] "OUR Sample Resume 2.docx"
## [800] "p. 150 (1).docx"
## [801] "p. 150.docx"
## [802] "pAG303 GPD EGFP ccdB (1).ape"
## [803] "pAG303 GPD EGFP ccdB.ape"
## [804] "Paragraphe d'auto-evaluation (1).docx"
## [805] "Paragraphe d'auto-evaluation.docx"
## [806] "Part B Lab 3 Data.pdf"
## [807] "Participation 3 (1).docx"
## [808] "Participation 3.docx"
## [809] "Participation2 (1).docx"
## [810] "Participation2.docx"
## [811] "PARTICIPATIONasynchronous_synchronous (1).docx"
## [812] "PARTICIPATIONasynchronous_synchronous (2).docx"
## [813] "PARTICIPATIONasynchronous_synchronous (3).docx"
## [814] "PARTICIPATIONasynchronous_synchronous (4).docx"
## [815] "PARTICIPATIONasynchronous_synchronous (5).docx"
## [816] "PARTICIPATIONasynchronous_synchronous.docx"
## [817] "PARTIEL aut20 copy.mp3"
## [818] "Pathways Results.pdf"
## [819] "Payslip - Wesley - 2022.11.04.pdf"
## [820] "PCA-missing_data.Rmd"
## [821] "PCR_agarose_gel (1).docx"
## [822] "PCR_agarose_gel (2).docx"
## [823] "PCR_agarose_gel.docx"
## [824] "PCR_DNA (1).xlsx"
## [825] "PCR_DNA (2).xlsx"
## [826] "PCR_DNA (3).xlsx"
## [827] "PCR_DNA.xlsx"
## [828] "PCR_protocol.docx"
## [829] "PCR_protocol_updated_1-31-22.docx"
## [830] "PCR_Reactions (1).xlsx"
## [831] "PCR_Reactions.xlsx"
## [832] "PDFConverter Installation (1).exe"
## [833] "PDFConverter Installation (2).exe"
## [834] "PDFConverter Installation (3).exe"
## [835] "PDFConverter Installation (4).exe"
## [836] "PDFConverter Installation (5).exe"
## [837] "PDFConverter Installation.exe"
## [838] "pDONR221.ape"
## [839] "Persuasive Speech.docx"
## [840] "pET16b sequence copy.xdna"
## [841] "pET16b.ape"
## [842] "phage (1).fasta"
## [843] "phage.fasta"
## [844] "Pham15821Report.pdf"
## [845] "Pham16216Report.pdf"
## [846] "Pham49320Report.pdf"
## [847] "pic_1603196844404.jpg"
## [848] "Picture-1.jpg"
## [849] "PITT_TSRPT.pdf"
## [850] "Pittsburgh HIV History .pdf"
## [851] "PlacementDesAdjectifs (1).docx"
## [852] "PlacementDesAdjectifs (2).docx"
## [853] "PlacementDesAdjectifs.docx"
## [854] "Plan - semaine 8.docx"
## [855] "Plasmid_DNA (1).xlsx"
## [856] "Plasmid_DNA (2).xlsx"
## [857] "Plasmid_DNA.xlsx"
## [858] "PlasmidRecitation.jpg"
## [859] "plasmids-1.pptx"
## [860] "plot_errorplot_Meillere_et_al_2015_telomeres.pdf"
## [861] "plots_4types_Meillere_et_al_2015_telomeres.pdf"
## [862] "pod38vines (1).mproj"
## [863] "pod38vines (2).mproj"
## [864] "pod38vines.mproj"
## [865] "poliscifi-reading-Tiptree-Houston, Houston, Do You Read (1).pdf"
## [866] "Pop Culture Analysis Peer Review.docx"
## [867] "Pop Culture Essay (1).docx"
## [868] "Pop Culture Essay (2).docx"
## [869] "Pop Culture Essay (3) (1).docx"
## [870] "Pop Culture Essay (3) (2).docx"
## [871] "Pop Culture Essay (3).docx"
## [872] "Pop Culture Essay.docx"
## [873] "portfolio_ggpubr_intro-2 (1).Rmd"
## [874] "portfolio_ggpubr_intro-2.Rmd"
## [875] "portfolio_ggpubr_log_transformation.Rmd"
## [876] "post_recitation_wk06 (1).pdf"
## [877] "post_recitation_wk06.pdf"
## [878] "Pou5f1 distal enhancer 1 SB left (equal).xdna"
## [879] "Pou5f1 landscape.png"
## [880] "Pourquoi je ne pourrais finalement pas vivre à Paris _! - Maghily.pdf"
## [881] "Practice_Exam 3_Key.pdf"
## [882] "PRE-COLONIAL AFRICAN HISTORY AND MISCONCEPTION OF AFRICA.pdf"
## [883] "pre_recitation_homework_1_part2.pdf"
## [884] "pre_recitation_wk06-PDF (1).pdf"
## [885] "pre_recitation_wk06-PDF (2).pdf"
## [886] "pre_recitation_wk06-PDF (3).pdf"
## [887] "pre_recitation_wk06-PDF (4).pdf"
## [888] "pre_recitation_wk06-PDF.pdf"
## [889] "Présidentielles française et américaine _ semblables et si différentes - Mémoire des luttes.pdf"
## [890] "Primers.xlsx"
## [891] "Problem set 1 revision 072722.pdf"
## [892] "Problem set 1.pdf"
## [893] "Project 3 (1).docx"
## [894] "Project 3.docx"
## [895] "Project Proposal_SH (1).docx"
## [896] "Project Proposal_SH.docx"
## [897] "Projet 1 (1) (1).pdf"
## [898] "Projet 1 (1) Mika.docx"
## [899] "Projet 1 (1).docx"
## [900] "Projet 1 (1).pdf"
## [901] "Projet 1.docx"
## [902] "Projet 1.pdf"
## [903] "Projet 2.docx"
## [904] "Qi_2013_originalCRISPRi.pdf"
## [905] "qPCR.xlsx"
## [906] "R-4.2.1-win.exe"
## [907] "R.ape"
## [908] "racial-bias-in-pain-assessment-and-treatment-recommendations,-and-false-beliefs-about-biological-differences-between-blacks-and-whites (1).ris"
## [909] "racial-bias-in-pain-assessment-and-treatment-recommendations,-and-false-beliefs-about-biological-differences-between-blacks-and-whites.bib"
## [910] "racial-bias-in-pain-assessment-and-treatment-recommendations,-and-false-beliefs-about-biological-differences-between-blacks-and-whites.ris"
## [911] "rates_intro-1.pdf"
## [912] "raw.png"
## [913] "RD02-1-22_Restriction_digest_agarose_gel (1).docx"
## [914] "RD02-1-22_Restriction_digest_agarose_gel.docx"
## [915] "RD03-1-22.docx"
## [916] "Recitation - 1 - Answer Key.pdf"
## [917] "Recitation - 1 - Practice Problems.pdf"
## [918] "Recitation 2_Chapter 14 Additional Problems_KEY.pdf"
## [919] "Recitation 4_Chapter 16 Additional Problems.pdf"
## [920] "recitation_exercise_Meillere_et_al_2015_FLEXPITT.pdf"
## [921] "recitation11_HWE_flowchart_vs1.pdf"
## [922] "recitation4KEY.pdf"
## [923] "Reflection-Questions-Volunteer-Social.doc"
## [924] "Reflection (1).docx"
## [925] "Reflection (2).docx"
## [926] "Reflection Paper 1.docx"
## [927] "Reflection Paper 2.docx"
## [928] "Reflection Paper 2.odt"
## [929] "Reflection Paper 3 (1).docx"
## [930] "Reflection Paper 3.docx"
## [931] "Reflection.docx"
## [932] "removing_fixed_alleles.html"
## [933] "removing_fixed_alleles.Rmd"
## [934] "Research Concept Map.docx"
## [935] "Research Statement_final_SH.docx"
## [936] "Research Statement_SH.docx"
## [937] "Resonse Paper 1.docx"
## [938] "Response Paper 1 (1).docx"
## [939] "Response Paper 1.docx"
## [940] "Response Paper 2 (1) (1).docx"
## [941] "Response Paper 2 (1).docx"
## [942] "Response Paper 2 (2).docx"
## [943] "Response Paper 2.docx"
## [944] "Response Paper 3 (1) (1).docx"
## [945] "Response Paper 3 (1).docx"
## [946] "Response Paper 3.docx"
## [947] "Response Paper 4-1.docx"
## [948] "Response Paper 4.docx"
## [949] "Response Paper 5 (1).docx"
## [950] "Response Paper 5.docx"
## [951] "Response Paper 6.docx"
## [952] "Restriction_digest_agarose_gel (1).docx"
## [953] "Restriction_digest_agarose_gel (2).docx"
## [954] "Restriction_digest_agarose_gel (3).docx"
## [955] "Restriction_digest_agarose_gel.docx"
## [956] "Restriction_Digests (1).docx"
## [957] "Restriction_Digests (2).docx"
## [958] "Restriction_Digests.docx"
## [959] "Resume (1).docx"
## [960] "Resume (1).pdf"
## [961] "Resume (2).docx"
## [962] "Resume (2).pdf"
## [963] "Resume Kareem Wali.docx"
## [964] "Resume Peer Review Form PDF (1).pdf"
## [965] "Resume Peer Review Form PDF.pdf"
## [966] "Resume.docx"
## [967] "Resume.pdf"
## [968] "resume2.pdf"
## [969] "reverse.ape"
## [970] "Révision 2 Grammaire Corrigé.docx"
## [971] "Rithika_Sankar_CV.docx"
## [972] "RNA-Guided Human Genome Engineering via Cas9.pdf"
## [973] "rsconnect"
## [974] "RStudio-2022.07.1-554.exe"
## [975] "RStudio-2022.07.2-576.exe"
## [976] "rtools42-5355-5357.exe"
## [977] "Running_DNA_agarose_gels.docx"
## [978] "Running_DNA_agarose_gels_updated_2-4-22 (1).docx"
## [979] "Running_DNA_agarose_gels_updated_2-4-22 (2).docx"
## [980] "Running_DNA_agarose_gels_updated_2-4-22.docx"
## [981] "S0010782421004388.txt"
## [982] "S14-ELEC.docx"
## [983] "S21-doc cam Chap 14b (1).pdf"
## [984] "S21-doc cam Chap 14b.pdf"
## [985] "S21-doc cam Chap 18 A - oxides (1).pdf"
## [986] "S21-doc cam Chap 18 A - oxides.pdf"
## [987] "S21-doc cam Chap 18 B2 - nonmetals (1).pdf"
## [988] "S21-doc cam Chap 18 B2 - nonmetals.pdf"
## [989] "S21-doc cam Chap 18 C Fossil Fuels (1).pdf"
## [990] "S21-doc cam Chap 18 C Fossil Fuels.pdf"
## [991] "S21-doc cam Chap 18 D Metals (1).pdf"
## [992] "S21-doc cam Chap 18 D Metals.pdf"
## [993] "S21-doc cam solar cells (1).pdf"
## [994] "S21-doc cam solar cells.pdf"
## [995] "S21-HWCover10to11 (1).docx"
## [996] "S21-HWCover10to11.docx"
## [997] "S21-HWCover11to12 (1).docx"
## [998] "S21-HWCover11to12.docx"
## [999] "S21-HWCover12to13 (1).docx"
## [1000] "S21-HWCover12to13.docx"
## [1001] "S21-HWCover13to14 (1).docx"
## [1002] "S21-HWCover13to14.docx"
## [1003] "S21-HWCover1to2 (1).docx"
## [1004] "S21-HWCover1to2 (2)-1 (1).docx"
## [1005] "S21-HWCover1to2 (2)-1.docx"
## [1006] "S21-HWCover1to2 (2)-2.docx"
## [1007] "S21-HWCover1to2 (2) (1).docx"
## [1008] "S21-HWCover1to2 (2).docx"
## [1009] "S21-HWCover1to2.docx"
## [1010] "S21-HWCover2to3.docx"
## [1011] "S21-HWCover3to4 (1).docx"
## [1012] "S21-HWCover3to4 (2).docx"
## [1013] "S21-HWCover3to4.docx"
## [1014] "S21-HWCover4to5.docx"
## [1015] "S21-HWCover5to6-1 (1).docx"
## [1016] "S21-HWCover5to6-1.docx"
## [1017] "S21-HWCover6to7 (1).docx"
## [1018] "S21-HWCover6to7.docx"
## [1019] "S21-HWCover7to8 (1).docx"
## [1020] "S21-HWCover7to8 (2).docx"
## [1021] "S21-HWCover7to8 (3).docx"
## [1022] "S21-HWCover7to8.docx"
## [1023] "S21-HWCover8to9 (1).docx"
## [1024] "S21-HWCover8to9.docx"
## [1025] "S21-HWCover9to10 (1).docx"
## [1026] "S21-HWCover9to10.docx"
## [1027] "S21 Coverage of Openstax Chapters 18 19.docx"
## [1028] "S21 doc cam Chap 12 A2 (1).pdf"
## [1029] "S21 doc cam Chap 12 A2 (2).pdf"
## [1030] "S21 doc cam Chap 12 A2.pdf"
## [1031] "S21 doc cam Chap 12 B (1).pdf"
## [1032] "S21 doc cam Chap 12 B.pdf"
## [1033] "S21 doc cam Chap 12 C (1).pdf"
## [1034] "S21 doc cam Chap 12 C.pdf"
## [1035] "S21 doc cam Chap 15 (1).pdf"
## [1036] "S21 doc cam Chap 15.pdf"
## [1037] "Sabina Lawreniuk, “Climate Change Is Class War- Global labour’s challenge to the Capitalocene”.pdf"
## [1038] "Sample AAR - Honors Degree - 09-29-20.pdf"
## [1039] "sample exam 1 2221 answer key.pdf"
## [1040] "Santana Lardo CV.docx"
## [1041] "Sarah Stodola, The Last Resort- A Chronicle of Paradise, Profit, and Peril at the Beach, Chapters 6, 12, & Epilogue .pdf"
## [1042] "Schedule of Presentations 15APR22.doc"
## [1043] "SCIGRESS_V3.4.3_Windows64.exe"
## [1044] "Screen Shot 2021-01-20 at 5.17.30 PM.png"
## [1045] "Screen Shot 2021-01-20 at 5.18.12 PM.png"
## [1046] "Screen Shot 2021-01-20 at 5.18.21 PM.png"
## [1047] "Screen Shot 2021-08-27 at 12.15.39 PM.png"
## [1048] "Screenshot 2020-11-04 171623.png"
## [1049] "Screenshot 2020-11-04 174026.png"
## [1050] "Screenshot 2020-11-04 175124.png"
## [1051] "Screenshot 2020-11-11 153145.png"
## [1052] "Screenshot 2020-11-11 153303.png"
## [1053] "Screenshot 2021-04-15 153842.png"
## [1054] "Screenshot 2022-09-12 131952.png"
## [1055] "Screenshot 2022-09-12 132115.png"
## [1056] "Screenshot 2022-09-12 185107.png"
## [1057] "Screenshot 2022-09-12 185853.png"
## [1058] "Screenshot 2022-09-12 192954 (1).png"
## [1059] "Screenshot 2022-09-12 192954.png"
## [1060] "Screenshot 2022-09-28 145133.png"
## [1061] "Screenshot 2022-09-28 145206.png"
## [1062] "Screenshot 2022-09-29 103911.png"
## [1063] "Screenshot 2022-09-29 103930.png"
## [1064] "Screenshot 2022-09-29 103956.png"
## [1065] "Screenshot 2022-09-29 120710.png"
## [1066] "Screenshot 2022-09-29 122050.png"
## [1067] "Screenshot 2022-09-29 122114.png"
## [1068] "Screenshot 2022-09-29 122136.png"
## [1069] "Screenshot 2022-09-29 125355.png"
## [1070] "Screenshot 2022-09-29 125412.png"
## [1071] "Screenshot 2022-09-29 125710.png"
## [1072] "Screenshot 2022-09-29 132343.png"
## [1073] "Screenshot 2022-09-29 132406.png"
## [1074] "Screenshot 2022-09-29 132430.png"
## [1075] "Screenshot 2022-09-29 133332.png"
## [1076] "Screenshot 2022-09-29 165613.png"
## [1077] "Screenshot 2022-09-29 171257.png"
## [1078] "Screenshot 2022-09-30 103527.png"
## [1079] "Screenshot 2022-09-30 103646.png"
## [1080] "Screenshot 2022-09-30 104754.png"
## [1081] "Screenshot 2022-09-30 105052.png"
## [1082] "Screenshot 2022-09-30 105117.png"
## [1083] "Screenshot 2022-09-30 110137.png"
## [1084] "Screenshot 2022-09-30 110159.png"
## [1085] "Screenshot 2022-10-04 170939 (1).png"
## [1086] "Screenshot 2022-10-04 170939.png"
## [1087] "Screenshot 2022-10-06 160401.png"
## [1088] "Screenshot 2022-10-06 160416 (1).png"
## [1089] "Screenshot 2022-10-06 160416.png"
## [1090] "Screenshot 2022-10-13 123122 (1).png"
## [1091] "Screenshot 2022-10-13 123122.png"
## [1092] "Screenshot 2022-10-13 124330 (1).png"
## [1093] "Screenshot 2022-10-13 124330.png"
## [1094] "Screenshot 2022-10-16 214536.png"
## [1095] "Screenshot 2022-10-16 222514.png"
## [1096] "Screenshot 2022-10-16 222721.png"
## [1097] "Screenshot 2022-10-18 115408 (1).png"
## [1098] "Screenshot 2022-10-18 115408.png"
## [1099] "Screenshot 2022-10-19 140619 (1).png"
## [1100] "Screenshot 2022-10-19 140619.png"
## [1101] "Screenshot 2022-10-20 130146.png"
## [1102] "Screenshot 2022-10-20 162542.png"
## [1103] "Screenshot 2022-10-22 094330.png"
## [1104] "Screenshot 2022-10-22 100324.png"
## [1105] "Screenshot 2022-10-27 202844.png"
## [1106] "Screenshot 2022-10-31 153833 (1).png"
## [1107] "Screenshot 2022-10-31 153833.png"
## [1108] "Screenshot 2022-11-01 155909 (1).png"
## [1109] "Screenshot 2022-11-01 155909.png"
## [1110] "Screenshot 2022-11-02 092052.png"
## [1111] "Screenshot 2022-11-06 224145.png"
## [1112] "Screenshot 2022-11-06 224633.png"
## [1113] "Screenshot 2022-11-16 073356.png"
## [1114] "Screenshot 2022-11-16 083841.png"
## [1115] "Screenshot 2022-12-02 121232.png"
## [1116] "Screenshot 2022-12-03 235548.png"
## [1117] "Screenshot_20210608-004248.png"
## [1118] "Screenshot_20210816-202712_2.png"
## [1119] "Screenshot_20210818-195505_2.png"
## [1120] "Script (1).docx"
## [1121] "Script.docx"
## [1122] "sd-calculator.xlsx"
## [1123] "SEA Symposium (1).docx"
## [1124] "SEA Symposium.docx"
## [1125] "Sequence analysis 1 (1).docx"
## [1126] "Sequence analysis 1 (2).docx"
## [1127] "Sequence analysis 1.docx"
## [1128] "Sequence Analysis 2 (1).docx"
## [1129] "Sequence Analysis 2 (1).pdf"
## [1130] "Sequence Analysis 2 (2).docx"
## [1131] "Sequence Analysis 2.docx"
## [1132] "Sequence Analysis 3 (1).docx"
## [1133] "Sequence Analysis 3.docx"
## [1134] "sequencing D3R plasmids.pdf"
## [1135] "Sequencing_DNA_updated_2-2-22 (1).docx"
## [1136] "Sequencing_DNA_updated_2-2-22 (2).docx"
## [1137] "Sequencing_DNA_updated_2-2-22.docx"
## [1138] "Sexe, politique et puritanisme _ l'obsession américaine (1).pdf"
## [1139] "Sexe, politique et puritanisme _ l'obsession américaine (2).pdf"
## [1140] "Sexe, politique et puritanisme _ l'obsession américaine.pdf"
## [1141] "Short story essay (1).docx"
## [1142] "Short story essay (2).docx"
## [1143] "Short story essay.docx"
## [1144] "Six différences entre le capitalisme et le socialisme (1).docx"
## [1145] "Six différences entre le capitalisme et le socialisme.docx"
## [1146] "SlackSetup.exe"
## [1147] "Snapchat-1593651012.jpg"
## [1148] "Snapchat-278685887.jpg"
## [1149] "Snapchat-400739192.jpg"
## [1150] "Snapchat-640650776.jpg"
## [1151] "Socialisme et libéralisme, du rêve à la réalité _ Contrepoints.pdf"
## [1152] "Solastalgia.pdf"
## [1153] "SP 2021_Final Exam_Key.pdf"
## [1154] "Spring 2022_Exam 1_Key.pdf"
## [1155] "Spring 2023 FHC Fellowship.docx"
## [1156] "Spring 2023 FHC Fellowship_SH.docx"
## [1157] "spring 2023 schedule.png"
## [1158] "sqlite-dll-win32-x86-3360000 (1).zip"
## [1159] "sqlite-dll-win32-x86-3360000 (2).zip"
## [1160] "sqlite-dll-win32-x86-3360000 (3)"
## [1161] "sqlite-dll-win32-x86-3360000 (3).zip"
## [1162] "sqlite-dll-win32-x86-3360000 (4)"
## [1163] "sqlite-dll-win32-x86-3360000 (4).zip"
## [1164] "sqlite-dll-win32-x86-3360000.zip"
## [1165] "sqlite-tools-win32-x86-3360000.zip"
## [1166] "sqlitestudio-3.3.3 (1).zip"
## [1167] "sqlitestudio-3.3.3 (2).zip"
## [1168] "sqlitestudio-3.3.3 (3)"
## [1169] "sqlitestudio-3.3.3 (3).zip"
## [1170] "sqlitestudio-3.3.3.zip"
## [1171] "Statement of Interest 4.docx"
## [1172] "statement of interest research class (1).docx"
## [1173] "statement of interest research class.docx"
## [1174] "Streak_out_bacteria_on_plates.docx"
## [1175] "Student Guide-for-Digital-Portfolio-Global Studies.docx"
## [1176] "Student_compound_microscope (1).docx"
## [1177] "Student_compound_microscope.docx"
## [1178] "SURACover.docx"
## [1179] "SURP Personal Statement.docx"
## [1180] "SURP+Personal+Statement.docx"
## [1181] "Syllabus for French 106.pdf"
## [1182] "TableauDesktop-64bit-2021-3-1.exe"
## [1183] "takeout-20200524T181118Z-001.zip"
## [1184] "tandf_riij2019_17 (1).bib"
## [1185] "tandf_riij2019_17.bib"
## [1186] "targetgene.ape"
## [1187] "TB523.pdf"
## [1188] "Teams_windows_x64.exe"
## [1189] "telomere_reading_assignment.pdf"
## [1190] "Thank you letter.docx"
## [1191] "the expression clone.ape"
## [1192] "The_Women_Men_Dont_See.pdf"
## [1193] "this_message_in_html (1).html"
## [1194] "this_message_in_html (2).html"
## [1195] "this_message_in_html (3).html"
## [1196] "this_message_in_html (4).html"
## [1197] "this_message_in_html.html"
## [1198] "Time Schedule Planner - A&S (1).docx"
## [1199] "Time Schedule Planner - A&S.docx"
## [1200] "Tiptree_Girl_Plugged_In.pdf"
## [1201] "Top Flower 2.jpeg"
## [1202] "Top Flower.jpeg"
## [1203] "Topic 1 climate change paper (Mayor et al. 2017).pdf"
## [1204] "Topic 1 Outline & Objectives.pdf"
## [1205] "Topic 1 PPT - Intro, Climate & Biomes (student).pptx"
## [1206] "Topic 2 Outline & Objectives.pdf"
## [1207] "Topic 2 PPT - Evolution (student).pptx"
## [1208] "Topic 7 PPT - Population distributions (student).pptx"
## [1209] "Transformation_of_E.coli_updated_2-21-22.docx"
## [1210] "transpose_VCF_data.html"
## [1211] "transpose_VCF_data.Rmd"
## [1212] "Troubleshooting and Progress July11.pptx"
## [1213] "Troubleshooting and Progress Aug8.pptx"
## [1214] "Troubleshooting and Progress May25.pptx"
## [1215] "Troubleshooting_and_Progress_June2.pptx"
## [1216] "TTseq_Master_Reaction_Spreadsheet (1).xlsx"
## [1217] "TTseq_Master_Reaction_Spreadsheet (2).xlsx"
## [1218] "TTseq_Master_Reaction_Spreadsheet.xlsx"
## [1219] "twinkle.jpg"
## [1220] "UngFR0221v3Fall2021 (1).docx"
## [1221] "UngFR0221v3Fall2021 (2).docx"
## [1222] "UngFR0221v3Fall2021.docx"
## [1223] "Unit4_minitest_practice_test_key-no_markup.pdf"
## [1224] "Untitled.png"
## [1225] "UTUavH11-1.docx"
## [1226] "UTUavH13.docx"
## [1227] "UTUavH2a-1 (1).docx"
## [1228] "UTUavH2a-1.docx"
## [1229] "UTUavH4-1.docx"
## [1230] "vcfR_test.vcf"
## [1231] "vcfR_test.vcf.gz"
## [1232] "vegan_PCA_amino_acids-STUDENT (1).Rmd"
## [1233] "vegan_PCA_amino_acids-STUDENT (2).Rmd"
## [1234] "vegan_PCA_amino_acids-STUDENT.Rmd"
## [1235] "vegan_pca_with_msleep-STUDENT--1-.html"
## [1236] "vegan_pca_with_msleep-STUDENT (1).Rmd"
## [1237] "vegan_pca_with_msleep-STUDENT.docx"
## [1238] "vegan_pca_with_msleep-STUDENT.Rmd"
## [1239] "video1675517822 (1).mp4"
## [1240] "video1675517822.mp4"
## [1241] "Vocab List.docx"
## [1242] "Vocabulaire _ frontière et identité.pdf"
## [1243] "walsh2017morphology (1).csv"
## [1244] "Wed Nov 04 2020 6_06_13 PM (1).webm"
## [1245] "Wed Nov 04 2020 6_06_13 PM (2)(1).webm"
## [1246] "Wed Nov 04 2020 6_06_13 PM.webm"
## [1247] "Week 11 Annotation presentation and intro to covid variants full slides.pptx"
## [1248] "Week 13 AA substitution protein analysis full slides.pptx"
## [1249] "Week 2 Breakout session slides.pptx"
## [1250] "Week 3 Cover and HW Pdf.pdf"
## [1251] "Week 4 BLAST breakout slides Wed.pptx"
## [1252] "Week 5 Start tool Breakout slides.pptx"
## [1253] "Week 7 Function breakout slides.pptx"
## [1254] "Week 8 frameshifts breakout slides.pptx"
## [1255] "Week 9 Guiding Principles Floral slides (1).pptx"
## [1256] "Week 9 Guiding Principles Floral slides (2).pptx"
## [1257] "Week 9 Guiding Principles Floral slides (3).pptx"
## [1258] "Week 9 Guiding Principles Floral slides.pptx"
## [1259] "week11_handout.pdf"
## [1260] "Weekly Time Management Schedule (1).xlsx"
## [1261] "Weekly Time Management Schedule.xlsx"
## [1262] "Wesley-Final Report-2022-1-1.docx"
## [1263] "Wesley-Final Report-2022-1 (1).docx"
## [1264] "Wesley-Final Report-2022-1 (2).docx"
## [1265] "Wesley-Final Report-2022-1.docx"
## [1266] "Wesley Resume (1).docx"
## [1267] "Wesley Resume.docx"
## [1268] "Wesley_Summer 2022 Fellowship Letter (1).pdf"
## [1269] "Wesley_Summer 2022 Fellowship Letter.pdf"
## [1270] "Who are the gilets jaunes and what do they want_ _ France _ The Guardian.pdf"
## [1271] "Will Conroy's Notes Chapter V.pdf"
## [1272] "wk07_recitation_plasmids-KEY.pdf"
## [1273] "wolves_answer_templates (1).pdf"
## [1274] "wolves_answer_templates.pdf"
## [1275] "Word File-26.docx"
## [1276] "Word File-32.docx"
## [1277] "Word File-7.docx"
## [1278] "Word File-8.docx"
## [1279] "working_directory_practice (1).Rmd"
## [1280] "working_directory_practice.Rmd"
## [1281] "Yeo_dCas9plasmids.pdf"
## [1282] "Your File Is Ready To Download.vhd"
## [1283] "Your Work.jpeg"
## [1284] "Zeiss_Compound_microscopes_epifluorescence_cameras_v1.1 (1).pptx"
## [1285] "Zeiss_Compound_microscopes_epifluorescence_cameras_v1.1.pptx"
## [1286] "Zoom_cm_fiisiZ9vvrZo4_mX9ECbv1ZEkEMZF+UUOkrDGyeiZp6W5prBWMS@EaezZkzDPa+yaQS2_kfdcf9dc3b617a3fb_.exe" # TODOIf you have lots of files in the working directory, you can search for the file specifically with list.files(pattern = “walsh”)
list.files(pattern = "walsh")## [1] "walsh2017morphology (1).csv" # TODOCSV files can be read in with the read.csv()
function.
# add read.csv() to load the file
setwd("C:/Users/mikaw/OneDrive/Pitt/Computational Biology/my_snps")
df <- read.csv(file = "walsh2017morphology.csv") # TODOAlways check to make sure the data looks like what you expected with
head(), summary() and other functions.
# run head(), summary(), and dim() on the data
head(df)## spp wing bill weight
## 1 NESP 56 8.5 18.2
## 2 NESP 56 8.5 20.7
## 3 NESP 59 8.0 17.6
## 4 NESP 59 8.2 16.0
## 5 NESP 60 8.3 16.5
## 6 NESP 58 8.5 16.0summary(df)## spp wing bill weight
## Length:73 Min. :53.00 Min. :7.900 Min. :14.5
## Class :character 1st Qu.:56.00 1st Qu.:8.400 1st Qu.:16.0
## Mode :character Median :57.00 Median :8.600 Median :17.0
## Mean :57.01 Mean :8.782 Mean :17.4
## 3rd Qu.:58.00 3rd Qu.:9.240 3rd Qu.:18.9
## Max. :60.00 Max. :9.900 Max. :21.7
## NA's :10 NA's :10 NA's :12dim(df)## [1] 73 4 # TODOWhen doing PCA on SNPs you have to consider the possibility that a SNP is fixed and all values in a column are identical. This is not typically an issue for conventional datasets like the morphology data we are working with here. When doing large-scale analyses with 1000s of columns and limits on computational power it would be advisable to check for invariant columns, which could be due to some feature of the data you aren’t aware of or an error in data processing.
We always scale data for PCA. This could be done before or after dealing with NAs and other data preparation issues.
The first column is character data so we’ll drop that when scaling
using df[, -1].
# make a copy of the dataframe
df2_scale <- df
# add scale() to scale the data
df2_scale[,-1] <- scale(df[,-1]) We need to remove NAs with na.omit(). We could impute
the missing data, but there aren’t too many values that are missing. (We
could use a for() loop to do the imputation if we wanted, or my function
mean_imputation())
# add na.omit() to remove the NAs
# assign the output to df2_scale_noNA
df2_scale_noNA <- na.omit(df2_scale) #TODOWe can run a PCA with prcomp(). The first column is
character data so [,-1] is included to that prcomp() doesn’t get it.
# add prcomp() and assign it to an object called
## morpho_pca
morpho_pca <- prcomp(df2_scale_noNA[,-1]) #TODOIts important to assess some things from the PCA output before moving forward with interpreting a plot of the PCA results such as a biplot. These are generally called performance diagnostics.
It is important when doing PCA to decide how many of the new, re-engineered dimensions should be retained. PCA does not inherently reduce the dimensionality of a dataset. If you put in a dataframe with 10 columns into prcomp(), you get 10 PCs (10 dimensions) out of it. Its the job of the data analyst to decide how many of the new features (PCs) should be considered, plot, and/or used in further analyses.
A scree plot is the typical tool for this. The base R scree plot is pretty basic. In general, we’re looking for a steep drop between two PCs. The PCs before the drop are most worthwhile to examine.
# add screeplot() to make the scree plot
screeplot(morpho_pca) #TODO
The bars on the default R scree plot represent the relative importance of the PCs in representing the data.
More specifically, they are proportional to the amount of variation in the data captured by each PC. The more variation represented by a PC, the more important it is.
We can get the information on the percentage of variation in the data
using the summary() command.
First, we get the summary information and store it to an object.
# call summary()
summary_out_morpho <- summary(morpho_pca) #TODOThen we use a function to extract the information on explained variation (importance) we want.
# add return(var_explained) to get output
PCA_variation <- function(pca_summary, PCs = 2){
var_explained <- pca_summary$importance[2,1:PCs]*100
var_explained <- round(var_explained,1)
return(var_explained) # TODO
}This function allows us to specify how many PCs2 we want. The default is 2 PCs, since that is what is usually plotted. Let’s get the first 3 PCs because that’s all there are in these morphological data.
# call PCA_variation(), with PCs = 3
var_out <- PCA_variation(summary_out_morpho, # TODO
PCs = 3)
var_out## PC1 PC2 PC3
## 55.1 32.0 12.8This means that PC1 captures 55.1% of the variation in the data. PC2 captures only 32%, and PC3 captures 12.8%.
These percentages are often reported as labels on biplots and scatterplots of PCA results (See below).
They can also be used to decide how many PCs to work with.
Instead of the default screeplot, we can make a screeplot where the y-axis is the percent of variation captured by each PC. We’ll use the barplot() function to do this.
# number of dimensions in the data
N_columns <- ncol(df2_scale_noNA)
# make barplot
barplot(var_out,
main = "Percent variation Scree plot",
ylab = "Percent variation explained")
abline(h = 1/N_columns*100, col = 2, lwd = 2)
The horizontal line in the barplot is calculated as 100/(# of dimensions in the data) If all the PCs were equally important, then the amount of variation they would explain would be (100)/(# of columns). These data have 3 columns, so if all the PCs were equal, they would each explain 33% of the variation. A general rule of them is to focus on PCs that explain more than this percentage.
Now we’ll make the biplot. Look at the biplot and interpret the relationship between the 3 features bill, weight, and wing. Then read the information below.
# add biplot() to see the biplot
biplot(morpho_pca) #TODO
Note that if the arrows aren’t plotted, its not a biplot.
Get the scores:
# call vegan::scores()
morpho_scores <- vegan::scores(morpho_pca) # TODOCombine the scores with the species information into a dataframe.
# call data.frame()
morpho_scores2 <- data.frame(spp = df2_scale_noNA$spp,
morpho_scores)Plot the scores, with species color-coded
# make color and shape = "spp"
ggpubr::ggscatter(data = morpho_scores2,
y = "PC2",
x = "PC1",
color = "spp", # TODO
shape = "spp", # TODO
main = "PCA Scatterplot",
xlab = "PC1 (55.1% of variation",
ylab = "PC2 (32% of variation)")
Note how in the plot the amount of variation explained by each PC is shown in the axis labels.
In the biplot created above, the “bill” and “weight” vectors point to the left, and “wing” points straight down.
This means that bill and weight are correlated with PC1, which is always the horizontal axis. Wing is correlated with PC2, the vertical axis.
Bill and weight are very close to each other, so the raw data of these features are going to be highly correlated with each other.
The “Wing” vector points straight down at a about a 90 degree (right) angle to not only PC1, but also bill and weight. We can therefore say that the wing vector is orthogonal to PC1, bill, and weight.