query.miR <- GDCquery(project = "TCGA-BRCA",
data.category = "Gene expression",
data.type = "miRNA gene quantification",
legacy = TRUE)## [1] "TCGA-3C-AAAU-01A-11R-A41G-13.hg19.mirbase20.mirna.quantification.txt"
## [2] "TCGA-3C-AAAU-01A-11R-A41G-13.mirna.quantification.txt"
## [3] "TCGA-3C-AALI-01A-11R-A41G-13.hg19.mirbase20.mirna.quantification.txt"
## [4] "TCGA-3C-AALI-01A-11R-A41G-13.mirna.quantification.txt"
## [5] "TCGA-3C-AALJ-01A-31R-A41G-13.hg19.mirbase20.mirna.quantification.txt"
## [6] "TCGA-3C-AALJ-01A-31R-A41G-13.mirna.quantification.txt"query.miR <- GDCquery(project = "TCGA-BRCA",
data.category = "Gene expression",
data.type = "miRNA gene quantification",
file.type = "hg19.mirbase20.mirna",
legacy = TRUE)## [1] "TCGA-3C-AAAU-01A-11R-A41G-13.hg19.mirbase20.mirna.quantification.txt"
## [2] "TCGA-3C-AALI-01A-11R-A41G-13.hg19.mirbase20.mirna.quantification.txt"
## [3] "TCGA-3C-AALJ-01A-31R-A41G-13.hg19.mirbase20.mirna.quantification.txt"
## [4] "TCGA-3C-AALK-01A-11R-A41G-13.hg19.mirbase20.mirna.quantification.txt"
## [5] "TCGA-4H-AAAK-01A-12R-A41G-13.hg19.mirbase20.mirna.quantification.txt"
## [6] "TCGA-5L-AAT0-01A-12R-A41G-13.hg19.mirbase20.mirna.quantification.txt"query.miR <- GDCquery(project = "TCGA-BRCA",
data.category = "Gene expression",
data.type = "miRNA gene quantification",
file.type = "mirna",
legacy = TRUE)## [1] "TCGA-3C-AAAU-01A-11R-A41G-13.mirna.quantification.txt"
## [2] "TCGA-3C-AALI-01A-11R-A41G-13.mirna.quantification.txt"
## [3] "TCGA-3C-AALJ-01A-31R-A41G-13.mirna.quantification.txt"
## [4] "TCGA-3C-AALK-01A-11R-A41G-13.mirna.quantification.txt"
## [5] "TCGA-4H-AAAK-01A-12R-A41G-13.mirna.quantification.txt"
## [6] "TCGA-5L-AAT0-01A-12R-A41G-13.mirna.quantification.txt"query.miR <- GDCquery(project = "TCGA-COAD",
data.category = "Gene expression",
data.type = "miRNA gene quantification",
legacy = TRUE)## [1] "TCGA-3L-AA1B-01A-11H-A37P-13.hg19.mirbase20.mirna.quantification.txt"
## [2] "TCGA-3L-AA1B-01A-11H-A37P-13.hg19.mirna.quantification.txt"
## [3] "TCGA-4N-A93T-01A-11H-A37P-13.hg19.mirbase20.mirna.quantification.txt"
## [4] "TCGA-4N-A93T-01A-11H-A37P-13.hg19.mirna.quantification.txt"
## [5] "TCGA-4T-AA8H-01A-11H-A41D-13.hg19.mirbase20.mirna.quantification.txt"
## [6] "TCGA-4T-AA8H-01A-11H-A41D-13.hg19.mirna.quantification.txt"query.miR <- GDCquery(project = "TCGA-COAD",
data.category = "Gene expression",
data.type = "miRNA gene quantification",
file.type = "hg19.mirbase20.mirna",
legacy = TRUE)## [1] "TCGA-3L-AA1B-01A-11H-A37P-13.hg19.mirbase20.mirna.quantification.txt"
## [2] "TCGA-4N-A93T-01A-11H-A37P-13.hg19.mirbase20.mirna.quantification.txt"
## [3] "TCGA-4T-AA8H-01A-11H-A41D-13.hg19.mirbase20.mirna.quantification.txt"
## [4] "TCGA-5M-AAT4-01A-11H-A41D-13.hg19.mirbase20.mirna.quantification.txt"
## [5] "TCGA-5M-AAT5-01A-21H-A41D-13.hg19.mirbase20.mirna.quantification.txt"
## [6] "TCGA-5M-AAT6-01A-11H-A41D-13.hg19.mirbase20.mirna.quantification.txt"query.miR <- GDCquery(project = "TCGA-COAD",
data.category = "Gene expression",
data.type = "miRNA gene quantification",
file.type = "hg19.mirna",
legacy = TRUE)## [1] "TCGA-3L-AA1B-01A-11H-A37P-13.hg19.mirna.quantification.txt"
## [2] "TCGA-4N-A93T-01A-11H-A37P-13.hg19.mirna.quantification.txt"
## [3] "TCGA-4T-AA8H-01A-11H-A41D-13.hg19.mirna.quantification.txt"
## [4] "TCGA-5M-AAT4-01A-11H-A41D-13.hg19.mirna.quantification.txt"
## [5] "TCGA-5M-AAT5-01A-21H-A41D-13.hg19.mirna.quantification.txt"
## [6] "TCGA-5M-AAT6-01A-11H-A41D-13.hg19.mirna.quantification.txt"## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 3.6.1 (2019-07-05)
## os Ubuntu 19.10
## system x86_64, linux-gnu
## ui X11
## language en_US
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2019-11-27
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib
## annotate 1.64.0 2019-10-29 [1]
## AnnotationDbi 1.48.0 2019-10-29 [1]
## aroma.light 3.16.0 2019-10-29 [1]
## askpass 1.1 2019-01-13 [2]
## assertthat 0.2.1 2019-03-21 [2]
## backports 1.1.5 2019-10-02 [2]
## base64enc 0.1-3 2015-07-28 [2]
## Biobase 2.46.0 2019-10-29 [1]
## BiocFileCache 1.10.0 2019-10-29 [1]
## BiocGenerics 0.32.0 2019-10-29 [1]
## BiocParallel 1.20.0 2019-10-30 [1]
## biomaRt 2.42.0 2019-10-29 [1]
## Biostrings 2.54.0 2019-10-29 [1]
## bit 1.1-14 2018-05-29 [2]
## bit64 0.9-7 2017-05-08 [2]
## bitops 1.0-6 2013-08-17 [2]
## blob 1.2.0 2019-07-09 [2]
## broom 0.5.2 2019-04-07 [2]
## callr 3.3.2 2019-09-22 [2]
## circlize 0.4.8 2019-09-08 [2]
## cli 1.1.0 2019-03-19 [2]
## clue 0.3-57 2019-02-25 [2]
## cluster 2.1.0 2019-06-19 [4]
## codetools 0.2-16 2018-12-24 [4]
## colorspace 1.4-1 2019-03-18 [2]
## ComplexHeatmap 2.3.1 2019-11-09 [2]
## ConsensusClusterPlus 1.50.0 2019-10-29 [1]
## crayon 1.3.4 2017-09-16 [2]
## curl 4.2 2019-09-24 [2]
## data.table 1.12.6 2019-10-18 [1]
## DBI 1.0.0 2018-05-02 [2]
## dbplyr 1.4.2 2019-06-17 [2]
## DelayedArray 0.12.0 2019-10-29 [1]
## desc 1.2.0 2018-05-01 [2]
## DESeq 1.38.0 2019-10-29 [1]
## devtools 2.2.1 2019-09-24 [2]
## digest 0.6.22 2019-10-21 [1]
## doParallel 1.0.15 2019-08-02 [2]
## downloader 0.4 2015-07-09 [2]
## dplyr * 0.8.3 2019-07-04 [2]
## EDASeq 2.20.0 2019-10-29 [1]
## edgeR 3.28.0 2019-10-29 [1]
## ellipsis 0.3.0 2019-09-20 [2]
## evaluate 0.14 2019-05-28 [2]
## foreach 1.4.7 2019-07-27 [2]
## fs 1.3.1 2019-05-06 [2]
## genefilter 1.68.0 2019-10-29 [1]
## geneplotter 1.64.0 2019-10-29 [1]
## generics 0.0.2 2018-11-29 [2]
## GenomeInfoDb 1.22.0 2019-10-29 [1]
## GenomeInfoDbData 1.2.2 2019-11-06 [1]
## GenomicAlignments 1.22.0 2019-10-29 [1]
## GenomicFeatures 1.38.0 2019-10-29 [1]
## GenomicRanges 1.38.0 2019-10-29 [1]
## GetoptLong 0.1.7 2018-06-10 [2]
## ggplot2 3.2.1.9000 2019-11-27 [2]
## ggpubr 0.2.4 2019-11-14 [2]
## ggrepel 0.8.1 2019-05-07 [2]
## ggsignif 0.6.0 2019-08-08 [2]
## ggthemes 4.2.0 2019-05-13 [2]
## GlobalOptions 0.1.1 2019-09-30 [2]
## glue 1.3.1 2019-03-12 [2]
## gridExtra 2.3 2017-09-09 [2]
## gtable 0.3.0 2019-03-25 [1]
## hms 0.5.2 2019-10-30 [2]
## htmltools 0.4.0 2019-10-04 [2]
## httr 1.4.1 2019-08-05 [2]
## hwriter 1.3.2 2014-09-10 [2]
## IRanges 2.20.0 2019-10-29 [1]
## iterators 1.0.12 2019-07-26 [2]
## jsonlite 1.6 2018-12-07 [2]
## km.ci 0.5-2 2009-08-30 [2]
## KMsurv 0.1-5 2012-12-03 [2]
## knitr 1.26 2019-11-12 [2]
## lattice 0.20-38 2018-11-04 [4]
## latticeExtra 0.6-28 2016-02-09 [2]
## lifecycle 0.1.0 2019-08-01 [2]
## limma 3.42.0 2019-10-29 [1]
## locfit 1.5-9.1 2013-04-20 [2]
## magrittr 1.5 2014-11-22 [2]
## matlab 1.0.2 2014-06-24 [2]
## Matrix 1.2-17 2019-03-22 [4]
## matrixStats 0.55.0 2019-09-07 [2]
## memoise 1.1.0 2017-04-21 [2]
## mgcv 1.8-31 2019-11-09 [4]
## munsell 0.5.0 2018-06-12 [2]
## nlme 3.1-142 2019-11-07 [4]
## openssl 1.4.1 2019-07-18 [2]
## parsetools 0.1.1 2019-07-11 [2]
## pillar 1.4.2 2019-06-29 [2]
## pkgbuild 1.0.6 2019-10-09 [2]
## pkgcond 0.1.0 2018-12-03 [2]
## pkgconfig 2.0.3 2019-09-22 [2]
## pkgload 1.0.2 2018-10-29 [2]
## plyr 1.8.4 2016-06-08 [2]
## png 0.1-7 2013-12-03 [2]
## postlogic 0.1.0 2018-11-26 [2]
## prettyunits 1.0.2 2015-07-13 [2]
## processx 3.4.1 2019-07-18 [2]
## progress 1.2.2 2019-05-16 [2]
## ps 1.3.0 2018-12-21 [2]
## purrr 0.3.3 2019-10-18 [1]
## purrrogress 0.1.1 2019-07-22 [2]
## R.methodsS3 1.7.1 2016-02-16 [2]
## R.oo 1.23.0 2019-11-03 [1]
## R.utils 2.9.0 2019-06-13 [2]
## R6 2.4.1 2019-11-12 [2]
## rappdirs 0.3.1 2016-03-28 [2]
## RColorBrewer 1.1-2 2014-12-07 [1]
## Rcpp 1.0.3 2019-11-08 [2]
## RCurl 1.95-4.12 2019-03-04 [2]
## readr 1.3.1 2018-12-21 [2]
## remotes 2.1.0 2019-06-24 [2]
## rjson 0.2.20 2018-06-08 [2]
## rlang 0.4.2 2019-11-23 [2]
## rmarkdown 1.16 2019-10-01 [1]
## rprojroot 1.3-2 2018-01-03 [2]
## Rsamtools 2.2.0 2019-10-29 [1]
## RSQLite 2.1.2 2019-07-24 [2]
## rtracklayer 1.46.0 2019-10-29 [1]
## rvest 0.3.5 2019-11-08 [2]
## S4Vectors 0.24.0 2019-10-29 [1]
## scales 1.1.0 2019-11-18 [2]
## selectr 0.4-2 2019-11-20 [2]
## sessioninfo 1.1.1 2018-11-05 [2]
## shape 1.4.4 2018-02-07 [2]
## ShortRead 1.44.0 2019-10-29 [1]
## stringi 1.4.3 2019-03-12 [2]
## stringr 1.4.0 2019-02-10 [2]
## SummarizedExperiment 1.16.0 2019-10-29 [1]
## survival 3.1-7 2019-11-09 [4]
## survminer 0.4.6 2019-09-03 [2]
## survMisc 0.5.5 2018-07-05 [2]
## sva 3.34.0 2019-10-29 [1]
## TCGAbiolinks * 2.15.1 2019-11-27 [2]
## testextra 0.1.0 2019-01-18 [2]
## testthat 2.3.0 2019-11-05 [2]
## tibble 2.1.3 2019-06-06 [2]
## tidyr 1.0.0 2019-09-11 [2]
## tidyselect 0.2.5 2018-10-11 [2]
## usethis 1.5.1 2019-07-04 [2]
## vctrs 0.2.0 2019-07-05 [2]
## withr 2.1.2 2018-03-15 [2]
## xfun 0.10 2019-10-01 [1]
## XML 3.98-1.20 2019-06-06 [2]
## xml2 1.2.2 2019-08-09 [2]
## xtable 1.8-4 2019-04-21 [2]
## XVector 0.26.0 2019-10-29 [1]
## yaml 2.2.0 2018-07-25 [2]
## zeallot 0.1.0 2018-01-28 [2]
## zlibbioc 1.32.0 2019-10-29 [1]
## zoo 1.8-6 2019-05-28 [2]
## source
## Bioconductor
## Bioconductor
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## CRAN (R 3.6.1)
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## [1] /home/tiagochst/R/x86_64-pc-linux-gnu-library/3.6
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