Package: gcapc 1.37.0

Mingxiang Teng

gcapc: GC Aware Peak Caller

Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.

Authors:Mingxiang Teng and Rafael A. Irizarry

gcapc_1.37.0.tar.gz
gcapc_1.37.0.zip(r-4.7)gcapc_1.37.0.zip(r-4.6)gcapc_1.37.0.zip(r-4.5)
gcapc_1.37.0.tgz(r-4.6-any)gcapc_1.37.0.tgz(r-4.5-any)
gcapc_1.37.0.tar.gz(r-4.7-any)gcapc_1.37.0.tar.gz(r-4.6-any)
gcapc_1.37.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
gcapc/json (API)

# Install 'gcapc' in R:

install.packages('gcapc', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/tengmx/gcapc/issues

On BioConductor:gcapc-1.37.0(bioc 3.24)gcapc-1.36.0(bioc 3.23)

sequencing chipseq batcheffect peakdetection

5.38 score 10 stars 16 scripts 7 exports 51 dependencies

Last updated from:16b89e7389. Checks:4 ERROR, 6 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	255
linux-devel-x86_64	OK	533
source / vignettes	OK	428
linux-release-x86_64	OK	550
macos-release-arm64	OK	364
macos-oldrel-arm64	OK	303
windows-devel	ERROR	461
windows-release	ERROR	416
windows-oldrel	ERROR	443
wasm-release	OK	238

Exports:bindWidth gcapcPeaks gcEffects peaksCAT read5endCoverage refinePeaks refineSites

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops BSgenome cigarillo codetools cpp11 crayon curl DelayedArray formatR futile.logger futile.options generics GenomicAlignments GenomicRanges httr IRanges jsonlite lambda.r lattice MASS Matrix MatrixGenerics matrixStats mime openssl R6 RCurl restfulr Rhtslib rjson Rsamtools rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys XML XVector yaml

The gcapc user's guide

Rendered fromgcapc.Rmdusingknitr::rmarkdown

Last update: 2017-06-08
Started: 2016-10-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ChIP-seq Binding Width And Peak Window Size Estimation	bindWidth
GC Effects Aware Peak Calling	gcapcPeaks
ChIP-seq GC Effects Estimation	gcEffects
CATplot of Peaks	peaksCAT
Reads Coverage Using 5-end Base	read5endCoverage
Refine Peaks with GC Effects	refinePeaks
Adjust ChIP-seq Read Count Table	refineSites