Overall
OLD
Done:
The first cell and gene quality control is in QC
The normalisation by deconvolution is in normalise
Feature selection and dimensional reduction in feature_selection_dimred
Clustering at different resolutions, clustering_01
First rough annotation in annotation_01
Cluster QC in clusterQC_k5, now includes doublets detection
Stricter cell and gene QC; dimensional reduction and feature selection with the cleaned data
Clustering with different resolutions clustering_02
Annotation annotation_02
Differential gene expression between WT and KO for each celltype DE_WT_KO_celltype and each cluster DE_WT_KO_k20
Differential abundance of cells between clusters between WT and KO:
Cell cycle in cell_cycle
Analyse Oligos separate in oligos, with DA in DA_oligo_miloR
Interactive Shinyapp with the analysis until this stage.
To Do/ In Progress
DEGs between MILO’s neighboorhoods?
YOUNG
The first cell and gene quality control is in QC_young
The normalisation by deconvolution is in normalise_young
Feature selection and dimensional reduction in feature_selection_dimred_young
Batch correction in batchcorrect_young
Clustering at different resolutions, clustering_01
First rough annotation in annotation_01
Stricter cell and gene QC; dimensional reduction and feature selection with the cleaned dataQC_norm_featrueselect_dimred_02
To Do/ In Progress
Clustering with different resolutions clustering_02 - try to get the BAMs separate from the other immune
Annotation annotation_02_res0.3
Differential gene expression (DE) between WT and KO and between WT and HETs for each cluster DE_WT_KO_HET_clusters and DE_WT_HET_microglia
Differential abundance of cells between clusters between WT KO and HET:
Using miloR, pairwise comparisons DA_miloR
Interactive Shinyapp with the analysis until this stage. - change colours
remove microglia background in DE?
DE using MAST?