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_summaryThis function allows you pull a summary information about...
completegets you an overlap of gene list with your object
dot_plot_topXgenesMake a dot plot for all your markers
Gene_contributionCalculate the contribution of each gene for the given gene...
Gene.gene.corheatmapheatmap for gene-gene correlation matrix
geom_split_violinggplot extension for split violin plot
get_embRun Velocyto analysis on your Seurat2 object
harmony_for_seuratuse the batch effect correction method harmony on Seurat...
hashtags_DEGThis function allows you to calculate DEG for the IG hashtags
Hglm.degapply DEG with multiple glms on Seruat object with case...
Isotypes_DEGThis function allows you to calculate DEG for the IG Isotypes
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_clonotypeThis function allows you to pull specific barcodes from the...
pull_hashtagThis function allows you to pull specific barcodes from the...
pull_isotypeThis function allows you to pull specific barcodes from the...
pull_vdjMerge clonotype and isotype data to GEX Seurat object
put_signatureCalculate average expression for gene set.
query_heatmapheatmap genes with certain function
Run_uMAPCalculate uMAP for Seurat object
save.plot_gridsave multiple gg plots in pdf
scanorama_seuratuse the batch effect correction method scanorama on Seurat...
Seurat2_monocle3Run Velocyto analysis on your Seurat2 object
Seurat2_velocytoRun Velocyto analysis on your Seurat2 object
Specific_hashtags_DEGThis function allows you to calculate DEG for some specific...
Specific_isotypes_DEGThis function allows you to calculate DEG for some specific...
SplitObjectSplits object into a list of subsetted objects.
throw_away_tagsmark tags that you think are useless as such
uMAPPlotPlot uMAP in 2 dimentions
umap_plot3dPlot your clusters in 3 dimensions
unarchive_10xPrepare 10x v3 out files files for Seurat 2
volcano_plplot volcano plot 2
volcano_pl2plot volcano plot 2
volcano_plotplor volcano plot
GrigoriiNos/rimmi.rnaseq documentation built on July 20, 2020, 5:22 p.m.