Package: HMMcopy 1.55.1
Andrew McPherson
HMMcopy: Copy number prediction with correction for GC and mappability bias for HTS data
Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.
Authors:
HMMcopy_1.55.1.tar.gz
HMMcopy_1.55.1.zip(r-4.7)HMMcopy_1.55.1.zip(r-4.6)HMMcopy_1.55.1.zip(r-4.5)
HMMcopy_1.55.1.tgz(r-4.6-x86_64)HMMcopy_1.55.1.tgz(r-4.6-arm64)HMMcopy_1.55.1.tgz(r-4.5-x86_64)HMMcopy_1.55.1.tgz(r-4.5-arm64)
HMMcopy_1.55.1.tar.gz(r-4.7-arm64)HMMcopy_1.55.1.tar.gz(r-4.7-x86_64)HMMcopy_1.55.1.tar.gz(r-4.6-arm64)HMMcopy_1.55.1.tar.gz(r-4.6-x86_64)
HMMcopy_1.55.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
HMMcopy/json (API)
| # Install 'HMMcopy' in R: |
| install.packages('HMMcopy', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- normal_copy - HMMcopy example dataset
- tumour_copy - HMMcopy example dataset
- tumour_param - HMMcopy example dataset
- tumour_reads - HMMcopy example dataset
- tumour_segments - HMMcopy example dataset
On BioConductor:HMMcopy-1.55.0(bioc 3.24)HMMcopy-1.54.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencingpreprocessingvisualizationcopynumbervariationmicroarray
Last updated from:0c9a92e4a0. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 132 | ||
| linux-devel-arm64 | NOTE | 130 | ||
| linux-devel-x86_64 | NOTE | 142 | ||
| source / vignettes | OK | 195 | ||
| linux-release-arm64 | NOTE | 118 | ||
| linux-release-x86_64 | NOTE | 147 | ||
| macos-release-arm64 | NOTE | 83 | ||
| macos-release-x86_64 | NOTE | 254 | ||
| macos-oldrel-arm64 | NOTE | 84 | ||
| macos-oldrel-x86_64 | NOTE | 169 | ||
| windows-devel | NOTE | 83 | ||
| windows-release | NOTE | 78 | ||
| windows-oldrel | NOTE | 85 | ||
| wasm-release | OK | 90 |
Exports:correctReadcountHMMsegmentplotBiasplotCorrectionplotParamplotSegmentsrangedDataToSegrangedDataToWigstateColswigsToRangedDatawigToArraywigToRangedData
Dependencies:data.table
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Bias-free copy number estimation and robust CNA detection in tumour samples from WGS HTS data | HMMcopy-package HMMcopy |
| Readcount correction for GC and mappability bias | correctReadcount |
| HMMcopy example dataset | HMMcopy-dataset normal_copy tumour tumour_copy tumour_param tumour_reads tumour_segments |
| Segmentation and classification of copy number profiles | HMMsegment |
| Visualization functions for correctReadcount results | plotBias plotCorrection plotParam plotSegments stateCols |
| WIG Import Functions | wigToArray wigToRangedData |
| WIG Output Functions | rangedDataToSeg rangedDataToWig |
| Parsing and sorting of uncorrected read and sequence information files | wigsToRangedData |
