Package: CSSQ 1.25.0

Fan Lab at Georgia Institute of Technology

CSSQ: Chip-seq Signal Quantifier Pipeline

This package is desgined to perform statistical analysis to identify statistically significant differentially bound regions between multiple groups of ChIP-seq dataset.

Authors:Ashwath Kumar [aut], Michael Y Hu [aut], Yajun Mei [aut], Yuhong Fan [aut]

CSSQ_1.25.0.tar.gz
CSSQ_1.25.0.zip(r-4.7)CSSQ_1.25.0.zip(r-4.6)CSSQ_1.25.0.zip(r-4.5)
CSSQ_1.25.0.tgz(r-4.6-any)CSSQ_1.25.0.tgz(r-4.5-any)
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CSSQ_1.25.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
CSSQ/json (API)

# Install 'CSSQ' in R:

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

On BioConductor:CSSQ-1.25.0(bioc 3.24)CSSQ-1.24.0(bioc 3.23)

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

chipseq differentialpeakcalling sequencing normalization

4.00 score 3 scripts 356 downloads 9 exports 77 dependencies

Last updated from:22f37523ca. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	220
linux-devel-x86_64	OK	374
source / vignettes	OK	269
linux-release-x86_64	OK	430
macos-release-arm64	OK	264
macos-oldrel-arm64	OK	238
windows-devel	OK	475
windows-release	OK	407
windows-oldrel	OK	418
wasm-release	OK	177

Exports:ansTransform DBAnalyze getBgSubVal getRegionCounts kmeansNormalize loadCountData normalizeData plotDist preprocessData

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray farver fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gtable httr IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig png R6 RColorBrewer RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo snow SparseArray SummarizedExperiment sys vctrs viridisLite withr XML XVector yaml

ChIP-seq signal quantifier (CSSQ)

Introduction | Processing summary | Example | Session Info

Rendered fromCSSQ.Rmdusingknitr::knitr

Last update: 2019-12-04
Started: 2019-11-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Perform quantification and normalization of count data	ansTransform
Calculates P-value for the regions	calculatePvalue
Calculates modified T-statistics values for the given label and comparison	calculateTvalue
Performs differential binding analysis	DBAnalyze
Perform quantification and normalization of count data	getBgSubVal
Identify possible combinations	getComparisons
Labels the samples according to the combinations from 'getComparisons'	getNewLabels
Quantify region level count data	getRegionCounts
Perform k-means clustering, normalize anscombe data and calculate cluster variances for a sample.	kmeansNormalize
Load count data from input file.	loadCountData
Normalize anscombe transformed data	normalizeData
Plot data distribution histograms	plotDist
Wrapper function to preprocess the data	preprocessData