Package: BaalChIP
Title: BaalChIP: Bayesian analysis of allele-specific transcription
        factor binding in cancer genomes
Description: The package offers functions to process multiple ChIP-seq
        BAM files and detect allele-specific events. Computes allele
        counts at individual variants (SNPs/SNVs), implements extensive
        QC steps to remove problematic variants, and utilizes a
        bayesian framework to identify statistically significant
        allele- specific events. BaalChIP is able to account for copy
        number differences between the two alleles, a known
        phenotypical feature of cancer samples.
Version: 1.36.0
Author: Ines de Santiago, Wei Liu, Ke Yuan, Martin O'Reilly, Chandra SR
        Chilamakuri, Bruce Ponder, Kerstin Meyer, Florian Markowetz
Maintainer: Ines de Santiago <inesdesantiago@gmail.com>
Depends: R (>= 3.3.1), GenomicRanges, IRanges, Rsamtools,
Imports: GenomicAlignments, GenomeInfoDb, doParallel, parallel, doBy,
        reshape2, scales, coda, foreach, ggplot2, methods, utils,
        graphics, stats
Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle
VignetteBuilder: knitr
License: Artistic-2.0
LazyData: true
RoxygenNote: 7.1.1
biocViews: Software, ChIPSeq, Bayesian, Sequencing
Config/pak/sysreqs: libbz2-dev libicu-dev liblzma-dev libssl-dev
        xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:34:21 UTC
RemoteUrl: https://github.com/bioc/BaalChIP
RemoteRef: RELEASE_3_22
RemoteSha: 4f4fba9cc7e83e2ddc956522820e59c588b06c08
NeedsCompilation: no
Packaged: 2026-02-26 09:00:40 UTC; root
Built: R 4.5.2; ; 2026-02-26 09:03:36 UTC; windows
