Introduction | Running the Pipeline | Running the Full Pipeline | Analyzing your results | Additional Options
Package: CNSigs 0.1.1
Shawn Striker
CNSigs: Analysis of Copy Number Signatures
A workflow to generate and analyze signatures based on copy number data using non-negative matrix factorization (NMF) in an approach similar to that used in mutational signatures. It can be used to extract features from Copy number segment data and use that to find a subset of copy number signatures which can be further used to correlate with other relevant data. For more on 'NMF' see Gaujoux (2013) <doi:10.1186/1471-2105-11-367>.
Authors:
CNSigs_0.1.1.tar.gz
CNSigs_0.1.1.tar.gz(r-4.7-any)CNSigs_0.1.1.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CNSigs/json (API)
| # Install 'CNSigs' in R: |
| install.packages('CNSigs', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- cancerComps - Components derived from TCGA
- cancerSigs - Signatures derived from TCGA
- collapsedSigs - Signatures derived from TCGA and collapsed.
- compsExp - Components fitted onto featsExp
- defaultFeats - Default features to use for copy number signatures
- featsExp - Features from segDataExp
- referenceExp - The result object from Pipeline using segDataExp.
- scmExp - Sample by component matrix for segDataExp
- segDataExp - Segmentation Data from TCGA BRCA samples
- sigExposExp - The generated sigExposure from the segDataExp run
- sigsExp - The generated Signatures from the segDataExp run
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:81232c8369. Checks:2 NOTE, 1 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | NOTE | 191 | ||
| source / vignettes | OK | 200 | ||
| linux-release-x86_64 | NOTE | 174 | ||
| wasm-release | FAIL | 149 |
Exports:addPloidyDatacompareExposurescreateSigsdetermineNumSigsdetSigNumPipelineextractCNFeatsfindExposuresfitComponentfitModelsgenerateSCMmatchSigsplotCompplotCompsplotScmplotSegsplotSigplotSigExposureplotSigExposureMatplotSigMatplotSigsreadSegsremapResultsrunPipelinesegStatssigSimsmoothSegsvalidateSegData
Dependencies:BiobaseBiocGenericsBiocManagercliclustercodetoolscolorspacecowplotcpp11digestdoParallelfarverflexmixforeachgenericsggplot2gluegridBasegtableisobanditeratorslabelinglatticelifecyclelseimagrittrmodeltoolsNMFnnetpheatmapplyrR6RColorBrewerRcppregistryreshape2rlangrngtoolsS7scalessnowstringistringrvctrsviridisLitewithr
