Files in yanwu2014/chromfunks

Functions for Analyzing Chromatin Accessibility Data

R/chrom.R R/coaccess.R R/deprecated.R R/diff_access.R R/gwas.R R/link_genes.R R/motif.R R/region_enrich.R R/utility.R README.md Scripts/TF_Analysis/01_THS_analysis.R Scripts/TF_Analysis/02_ATAC_THS_analysis.R Scripts/human_chimp/01_dA_motifs.R Scripts/scTHS/01_clustering_THS.R Scripts/scTHS/01_clustering_adult_THS.R Scripts/scTHS/02_In_subclustering.R Scripts/scTHS/02_RG_subclustering.R Scripts/scTHS/02_annotate_THS.R Scripts/sciATAC/01_reannotate_sciATAC.R Scripts/sciRNA/01_reannotate_sciRNA.R Scripts/snDrop/01_cluster_snDrop.R Tutorials/TF_networks_example.Rmd Tutorials/gChromVAR_example.Rmd man/AddLinkCorrelations.Rd man/CalcDiffAccess.Rd man/ChromRegionEnrich.Rd man/FilterConns.Rd man/FindCausalPeaks.Rd man/FindCausalProb.Rd man/FindLinkedGenes.Rd man/FindNearbyGenes.Rd man/GetBinCounts.Rd man/GetClusterAvg.Rd man/GetRegionCounts.Rd man/ImportCausalSNPs.Rd man/LogTFIDF.Rd man/MotifEnrich.Rd man/MotifRegionLinks.Rd man/PlotNetwork.Rd man/RegionChromVAR.Rd man/RegionGeneLinks.Rd man/RegionOverlapList.Rd man/RegionOverlapScores.Rd man/SubsetLinks.Rd man/TFGeneLinks.Rd man/TFRegionLinks.Rd man/TopDiffPeaks.Rd man/chromfunks-deprecated.Rd man/extend_gr.Rd man/extractField.Rd man/find_all_diff-deprecated.Rd man/flattenMat.Rd man/formatCisTopicPeaks.Rd man/geneAnno.Rd man/getBulkDev.Rd man/getPseudobulk.Rd man/granges2df.Rd man/granges2peak.Rd man/hello.Rd man/invertList.Rd man/invertListVector.Rd man/peak2df.Rd man/peak2granges.Rd man/simpleCap.Rd man/top_diff_peaks-deprecated.Rd man/unflattenVec.Rd