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:Daniel Lai, Gavin Ha, Sohrab Shah

HMMcopy_1.55.1.tar.gz
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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✨
DESCRIPTION
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'))

Datasets:

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-1.55.1(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.

sequencing preprocessing visualization copynumbervariation microarray

6.17 score 1 packages 163 scripts 18 mentions 12 exports 1 dependencies

Last updated from:0c9a92e4a0. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	134
linux-devel-arm64	NOTE	134
linux-devel-x86_64	NOTE	173
source / vignettes	OK	220
linux-release-arm64	NOTE	129
linux-release-x86_64	NOTE	134
macos-release-arm64	NOTE	101
macos-release-x86_64	NOTE	151
macos-oldrel-arm64	NOTE	81
macos-oldrel-x86_64	NOTE	165
windows-devel	NOTE	83
windows-release	NOTE	69
windows-oldrel	NOTE	89
wasm-release	OK	93

Exports:correctReadcount HMMsegment plotBias plotCorrection plotParam plotSegments rangedDataToSeg rangedDataToWig stateCols wigsToRangedData wigToArray wigToRangedData

Dependencies:data.table

HMMcopy

Rendered fromHMMcopy.Rnwusingutils::Sweave

Last update: 2021-11-22
Started: 2013-11-01

Citation

Development and contributors

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