Package: BaalChIP 1.33.0

Ines de Santiago

BaalChIP: BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

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.

Authors:Ines de Santiago, Wei Liu, Ke Yuan, Martin O'Reilly, Chandra SR Chilamakuri, Bruce Ponder, Kerstin Meyer, Florian Markowetz

BaalChIP_1.33.0.tar.gz
BaalChIP_1.33.0.zip(r-4.5)BaalChIP_1.33.0.zip(r-4.4)

BaalChIP_1.33.0.tar.gz(r-4.5-noble)BaalChIP_1.33.0.tar.gz(r-4.4-noble)
BaalChIP_1.33.0.tgz(r-4.4-emscripten)
BaalChIP.pdf |BaalChIP.html✨
BaalChIP/json (API)
NEWS

# Install 'BaalChIP' in R:
install.packages('BaalChIP', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On BioConductor:BaalChIP-1.31.0(bioc 3.20)BaalChIP-1.30.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

softwarechipseqbayesiansequencing

4.00 score 5 scripts 300 downloads 15 exports 89 dependencies

Last updated 23 days agofrom:6f46c6902a. Checks:OK: 1 WARNING: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winWARNINGOct 30 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winWARNINGOct 30 2024

Exports:adjustmentBaalPlotalleleCountsBaalChIPBaalChIP.getBaalChIP.reportBaalChIP.runfilter1allelefilterIntbiasgetASBmergePerGroupplotQCplotSimulQCfiltersummaryASBsummaryQC

Dependencies:abindaskpassbackportsBHBiobaseBiocGenericsBiocParallelBiostringsbitopsbootbroomclicodacodetoolscolorspacecowplotcpp11crayoncurlDelayedArrayDerivdoBydoParalleldplyrfansifarverforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobanditeratorsjsonlitelabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmicrobenchmarkmimemodelrmunsellnlmeopensslpillarpkgconfigplyrpurrrR6RColorBrewerRcppreshape2RhtslibrlangRsamtoolsS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

Ines de Santiago, Wei Liu, Ke Yuan, Florian Markowetz. University of Cambridge, Cancer Research UK Cambridge Institute

Rendered fromBaalChIP.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2021-03-01
Started: 2016-08-18

Readme and manuals

Help Manual

Help pageTopics
Method adjustmentBaalPlotadjustmentBaalPlot adjustmentBaalPlot,BaalChIP-method
Method alleleCountsalleleCounts alleleCounts,BaalChIP-method
BaalChIP-classBaalChIP
Method BaalChIP.getBaalChIP.get BaalChIP.get,BaalChIP-method
Method BaalChIP.reportBaalChIP.report BaalChIP.report,BaalChIP-method
Method BaalChIP.runBaalChIP.run BaalChIP.run,BaalChIP-method
BaalObject example datasetBaalObject
Blacklisted genomic regionsblacklist_hg19
ENCODEexample example datasetENCODEexample
FAIREexample example datasetFAIREexample
Method filter1allelefilter1allele filter1allele,BaalChIP-method
Method filterIntbiasfilterIntbias filterIntbias,BaalChIP-method
Method getASBgetASB getASB,BaalChIP-method
Method mergePerGroupmergePerGroup mergePerGroup,BaalChIP-method
Genomic regions of collapsed repeatspickrell2011cov1_hg19
Method plotQCplotQC plotQC,BaalChIP-method
Method plotSimulplotSimul plotSimul,BaalChIP-method
Method QCfilterQCfilter QCfilter,BaalChIP-method
Method summaryASBsummaryASB summaryASB,BaalChIP-method
Method summaryQCsummaryQC summaryQC,BaalChIP-method
Genomic regions of unique mappabilityUniqueMappability50bp_hg19