Man pages for ShixiangWang/VSHunter
Capture Variation Signatures from Genomic Data
| centromeres.hg19 | location of centromeres at genome build hg19 |
| centromeres.hg38 | location of centromeres at genome build hg38 |
| chromsize.hg19 | chromosome size of genome build hg19 |
| chromsize.hg38 | chromosome size of genome build hg38 |
| cnv_autoCaptureSignatures | Auto-capture signature and coresponding exposure |
| cnv_chooseSigNumber | Choose optimal number of signatures |
| cnv_derivefeatures | Derive copy number feature distributions |
| cnv_extractSignatures | Extract signature based on specified rank value |
| cnv_fitMixModels | Fit optimal number of mixture model components |
| cnv_generateSbCMatrix | Generate a sample-by-component matrix |
| cnv_getLengthFraction | Calculate length fraction profile of copy number |
| cnv_pipe | Calling CNV signature pipeline |
| cnv_plotDistributionProfile | Plot copy number distribution either by length or chromosome |
| cnv_plotFeatureDistribution | Plot copy number feature distribution |
| cnv_plotMixComponents | Plot mixture fit model components |
| cnv_plotSignatures | Plot CNV signatures |
| cnv_quantifySigExposure | Quantify exposure for samples using Linear Combination... |
| cnv_readprofile | Read copy number as a list of data.frame from data.frame or... |
| nmf_extract_group | Extract groups (sample clustering) from NMF run results |
| snv_extractSignatures | Extract mutational signatures from trinucleotide context. |
| snv_plotSignatures | Plots decomposed mutational signatures |
| snv_readprofile | Read MAF files. |
| snv_signatureEnrichment | Performs sample stratification based on signature... |
| snv_trinucleotideMatrix | Extract single 5' and 3' bases flanking the mutated site for... |
| VSHunter | VSHunter: A package for capturing variation signatures from... |
