all.abundance |
K-mer abundances |
AnnotateDBSVCF |
Add sequence context and transcript information to an in-memory DBS VCF |
AnnotateIDVCF |
Add sequence context to an in-memory ID (insertion/deletion) VCF, and confirm that they match the given reference genome |
AnnotateSBSVCF |
Add sequence context and transcript information to an in-memory SBS VCF |
as.catalog |
Create a catalog from a 'matrix', 'data.frame', or 'vector' |
Canonicalize1Del |
Given a deletion and its sequence context, categorize it |
catalog.row.order |
Standard order of row names in a catalog |
CatalogRowOrder |
Standard order of row names in a catalog |
Collapse144CatalogTo78 |
"Collapse" a catalog |
Collapse1536CatalogTo96 |
"Collapse" a catalog |
Collapse192CatalogTo96 |
"Collapse" a catalog |
CollapseCatalog |
"Collapse" a catalog |
FindDelMH |
Return the length of microhomology at a deletion |
FindMaxRepeatDel |
Return the number of repeat units in which a deletion is embedded |
gene.expression.data.HepG2 |
Example gene expression data from two cell lines |
gene.expression.data.MCF10A |
Example gene expression data from two cell lines |
GeneExpressionData |
Example gene expression data from two cell lines |
GetFreebayesVAF |
Extract the VAFs (variant allele frequencies) and read depth information from a VCF file |
GetMutectVAF |
Extract the VAFs (variant allele frequencies) and read depth information from a VCF file |
GetStrelkaVAF |
Extract the VAFs (variant allele frequencies) and read depth information from a VCF file |
GetVAF |
Extract the VAFs (variant allele frequencies) and read depth information from a VCF file |
ICAMS |
ICAMS: In-depth Characterization and Analysis of Mutational Signatures |
MutectVCFFilesToCatalog |
Create SBS, DBS and Indel catalogs from Mutect VCF files |
MutectVCFFilesToCatalogAndPlotToPdf |
Create SBS, DBS and Indel catalogs from Mutect VCF files and plot them to PDF |
MutectVCFFilesToZipFile |
Create a zip file which contains catalogs and plot PDFs from Mutect VCF files |
PlotCatalog |
Plot *one* spectrum or signature |
PlotCatalogToPdf |
Plot catalog to a PDF file |
PlotTransBiasGeneExp |
Plot transcription strand bias with respect to gene expression values |
PlotTransBiasGeneExpToPdf |
Plot transcription strand bias with respect to gene expression values to a PDF file |
ReadAndSplitMutectVCFs |
Read and split Mutect VCF files |
ReadAndSplitStrelkaSBSVCFs |
Read and split Strelka SBS VCF files |
ReadAndSplitVCFs |
Read and split VCF files |
ReadCatalog |
Read catalog |
ReadStrelkaIDVCFs |
Read Strelka ID (small insertion and deletion) VCF files |
revc |
Reverse complement every string in 'string.vec' |
StrelkaIDVCFFilesToCatalog |
Create ID (small insertion and deletion) catalog from Strelka ID VCF files |
StrelkaIDVCFFilesToCatalogAndPlotToPdf |
Create ID (small insertion and deletion) catalog from Strelka ID VCF files and plot them to PDF |
StrelkaIDVCFFilesToZipFile |
Create a zip file which contains ID (small insertion and deletion) catalog and plot PDF from Strelka ID VCF files |
StrelkaSBSVCFFilesToCatalog |
Create SBS and DBS catalogs from Strelka SBS VCF files |
StrelkaSBSVCFFilesToCatalogAndPlotToPdf |
Create SBS and DBS catalogs from Strelka SBS VCF files and plot them to PDF |
StrelkaSBSVCFFilesToZipFile |
Create a zip file which contains catalogs and plot PDFs from Strelka SBS VCF files |
trans.ranges.GRCh37 |
Transcript ranges data |
trans.ranges.GRCh38 |
Transcript ranges data |
trans.ranges.GRCm38 |
Transcript ranges data |
TranscriptRanges |
Transcript ranges data |
TransformCatalog |
Transform between counts and density spectrum catalogs and counts and density signature catalogs |
VCFsToCatalogs |
Create SBS, DBS and Indel catalogs from VCFs |
VCFsToCatalogsAndPlotToPdf |
Create SBS, DBS and Indel catalogs from VCFs and plot them to PDF |
VCFsToDBSCatalogs |
Create DBS catalogs from VCFs |
VCFsToIDCatalogs |
Create ID (small insertion and deletion) catalog from ID VCFs |
VCFsToSBSCatalogs |
Create SBS catalogs from SBS VCFs |
VCFsToZipFile |
Create a zip file which contains catalogs and plot PDFs from VCFs |
WriteCatalog |
Write a catalog |