Files in VCCRI/Sierra
PolyA counting and differential transcript usage analysis for scRNA-seq data
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/Annotate.R
R/count_polyA.R
R/data_util.R
R/dataset_merging.R
R/differential_usage.R
R/plotting_functions.R
R/split_bams.R
README.md
inst/extdata/Cxcl12_example.RData
inst/extdata/Cycling_vs_resting_fibro_UTR_length_res.RData
inst/extdata/TIP_cell_info.RData
inst/extdata/TIP_merged_peaks.txt
inst/extdata/TIP_vignette_gene_Seurat.RData
inst/extdata/Vignette_cellranger_genes_subset.gtf
inst/extdata/Vignette_example_TIP_MI_junctions.bed
inst/extdata/Vignette_example_TIP_mi.bai
inst/extdata/Vignette_example_TIP_mi.bam
inst/extdata/Vignette_example_TIP_sham.bam
inst/extdata/Vignette_example_TIP_sham.bam.bai
inst/extdata/Vignette_example_TIP_sham_junctions.bed
inst/extdata/example_TIP_MI_whitelist_barcodes.tsv
inst/extdata/example_TIP_sham_whitelist_barcodes.tsv
man/AggregatePeakCounts.Rd
man/AnnotatePeaksFromGTF.Rd
man/BaseComposition.Rd
man/CountPeaks.Rd
man/DUTest.Rd
man/DetectAEU.Rd
man/DetectUTRLengthShift.Rd
man/FindPeaks.Rd
man/GetExpressedPeaks.Rd
man/GetRelativeExpression.Rd
man/MergePeakCoordinates.Rd
man/NewPeakSCE.Rd
man/NewPeakSeurat.Rd
man/PeakSeuratFromTransfer.Rd
man/PlotCoverage.Rd
man/PlotRelativeExpressionBox.Rd
man/PlotRelativeExpressionTSNE.Rd
man/PlotRelativeExpressionUMAP.Rd
man/PlotRelativeExpressionViolin.Rd
man/PlotUTRLengthShift.Rd
man/ReadPeakCounts.Rd
man/SelectGenePeaks.Rd
man/SplitBam.Rd
man/annotate_gr_from_gtf.Rd
man/apply_DEXSeq_test_sce.Rd
man/apply_DEXSeq_test_seurat.Rd
man/do_arrow_plot.Rd
man/fit_gaussian.Rd
man/geneToGR.Rd
man/gene_Labels.Rd
man/generate_merged_peak_table.Rd
man/generate_self_merged_peaks.Rd
man/generate_self_similarity_table.Rd
man/generate_similarity_table.Rd
man/get_expressed_peaks_sce.Rd
man/get_expressed_peaks_seurat.Rd
man/get_relative_expression_sce.Rd
man/get_relative_expression_seurat.Rd
man/make_exons.Rd
man/make_reference.Rd
man/merge_bam_coverage.Rd
man/relative_location.Rd
man/rle_to_WIG.Rd
vignettes/Cxcl12_coverage_annotated.png
vignettes/DimPlot.png
vignettes/PlotCoverage_CXCL12.png
vignettes/PlotRelativeExpressionBox.png
vignettes/PlotRelativeExpressionTSNE.png
vignettes/PlotRelativeExpressionViolin.png
vignettes/Seurat.FeaturePlot.png
vignettes/Sierra_vignette.rmd
vignettes/UTRLengthPlot.png
