Package: csawBook 1.21.0

Aaron Lun

csawBook: The Book of csaw

Describes how to use the csaw package to detect differentially bound regions in ChIP-seq data. This provides instructions on how to read in BAM files to obtain a per-window count matrix, filtering to obtain high-abundance windows of interest, normalization of sample-specific biases, testing for differential binding, consolidation of per-window results to obtain per-region statistics, and annotation and visualization of the DB results.

Authors:Aaron Lun [aut, cre]

csawBook_1.21.0.tar.gz
csawBook_1.21.0.tar.gz(r-4.7-any)csawBook_1.21.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
csawBook/json (API)

# Install 'csawBook' in R:

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

On BioConductor:csawBook-1.21.0(books 3.24)csawBook-1.20.0(books 3.23)

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

workflow epigeneticsworkflow datapkg

4.00 score 0 exports 172 dependencies

Last updated from:37afce4d91. Checks:1 WARNING, 2 ERROR, 1 OK. Indexed: yes.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	WARNING	260
linux-devel	ERROR	266
source / vignettes	OK	3871
linux-release	ERROR	331

Exports:

Dependencies:abind AnnotationDbi AnnotationFilter AnnotationHub askpass backports base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocStyle BiocVersion biomaRt Biostrings biovizBase bit bit64 bitops blob bookdown BSgenome bslib cachem checkmate ChIPpeakAnno chipseqDBData cigarillo cli cluster CodeDepends codetools colorspace cpp11 crayon csaw curl data.table DBI dbplyr DelayedArray deldir dichromat digest dir.expiry dplyr edgeR ensembldb evaluate ExperimentHub farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue graph gridExtra gtable Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 InteractionSet interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise metapod mime multtest nnet openssl org.Mm.eg.db pillar pkgconfig png prettyunits progress ProtGenerics purrr pwalign R6 rappdirs RBGL RColorBrewer Rcpp RcppEigen RcppThread RCurl rebook regioneR restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors S7 sass scales Seqinfo snow SparseArray statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex TxDb.Mmusculus.UCSC.mm10.knownGene UCSC.utils universalmotif utf8 VariantAnnotation vctrs VennDiagram viridisLite withr xfun XML xml2 XVector yaml

Link to book

Rendered fromstub.Rmdusingknitr::rmarkdown

Last update: 2021-02-08
Started: 2020-11-08

Help page	Topics

Package: csawBook 1.21.0

csawBook: The Book of csaw

Citation

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Help Manual

Usage by other packages (reverse dependencies)