Package: HMMcopy 1.49.0
Daniel Lai
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_1.49.0.tar.gz
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HMMcopy.pdf |HMMcopy.html✨
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-1.49.0(bioc 3.21)HMMcopy-1.48.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
sequencingpreprocessingvisualizationcopynumbervariationmicroarray
Last updated 2 months agofrom:9dbb51b5c3. Checks:OK: 1 NOTE: 8. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win-x86_64 | NOTE | Nov 29 2024 |
| R-4.5-linux-x86_64 | NOTE | Nov 29 2024 |
| R-4.4-win-x86_64 | NOTE | Nov 29 2024 |
| R-4.4-mac-x86_64 | NOTE | Nov 29 2024 |
| R-4.4-mac-aarch64 | NOTE | Nov 29 2024 |
| R-4.3-win-x86_64 | NOTE | Nov 29 2024 |
| R-4.3-mac-x86_64 | NOTE | Nov 29 2024 |
| R-4.3-mac-aarch64 | NOTE | Nov 29 2024 |
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 |
