Man pages for GrigoriiNos/rimmi.rnaseq
Set of functions for genomics data analysis

add_hashMerge cell hashcoding demultiplexed data with GEX Seurat 3...
add_vdjMerge clonotype and isotype data to GEX Seurat object
all.genes.withGOGet all genes with partiular GO
annotate_markersAnnotation for the cell markers.
Cell.cell.corheatmapheatmap for cell-cell correlation matrix
cellphone_for_seuratcell-cell interaction analysis using method CellPhoneDB
clean_spmatRun Velocyto analysis on your Seurat2 object
clonotypes_summaryGives you a summary of your clonotypes
dot_plot_topXgenesMake a dot plot for all your markers
Gene.gene.corheatmapheatmap for gene-gene correlation matrix
geom_split_violinggplot extension for split violin plot
get_embRun Velocyto analysis on your Seurat2 object
Hglm.degapply DEG with multiple glms on Seruat object with case...
HTODemuxHTODemux in house modified Seurat::HTODemux for identifiyng...
hto.heatmaphto heatmap
lib.qc_plotPlot clusters in 2 umaps with the point size corresponting to...
list.to.tableunite list of deg table
markers_to_xlsgetting your markers into the excel shpreadsheet
merge_loomMerge two loom files into one and produce rvel.cd
preprocess_loomRun Velocyto analysis on your Seurat2 object
pseudo.bulk.DEGapply DESeq for DEG pseudo bulk collapsed samples
pull_vdjMerge clonotype and isotype data to GEX Seurat object
quantify_genesetsThis function allows you to calculate an average expression...
query_heatmapheatmap genes with certain function
rank_clonotypesRank clonotypes based of the spread in GEX space
save.plot_gridsave multiple gg plots in pdf
Seurat2_velocytoRun Velocyto analysis on your Seurat2 object
SplitObjectSplits object into a list of subsetted objects.
unarchive_10xPrepare 10x v3 out files files for Seurat 2
volcano_plplot volcano plot 2
volcano_pl2plot volcano plot 2
GrigoriiNos/rimmi.rnaseq documentation built on April 29, 2022, 5:18 p.m.