Package: CexoR 1.51.0

Pedro Madrigal

CexoR: An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Then, irreproducible discovery rate for overlapping peak-pairs across biological replicates is computed.

Authors:Pedro Madrigal [aut, cre]

CexoR_1.51.0.tar.gz
CexoR_1.51.0.zip(r-4.7)CexoR_1.51.0.zip(r-4.6)CexoR_1.51.0.zip(r-4.5)
CexoR_1.51.0.tgz(r-4.6-any)CexoR_1.51.0.tgz(r-4.5-any)
CexoR_1.51.0.tar.gz(r-4.7-any)CexoR_1.51.0.tar.gz(r-4.6-any)
CexoR_1.51.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
CexoR/json (API)

# Install 'CexoR' in R:

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

Bug tracker:https://github.com/pmb59/cexor/issues

On BioConductor:CexoR-1.51.0(bioc 3.24)CexoR-1.50.0(bioc 3.23)

functionalgenomics sequencing coverage chipseq peakdetection bioc-devel

4.95 score 1 scripts 1 mentions 4 exports 93 dependencies

Last updated from:9385e58314. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	227
linux-devel-x86_64	NOTE	439
source / vignettes	OK	327
linux-release-x86_64	NOTE	447
macos-release-arm64	NOTE	229
macos-oldrel-arm64	NOTE	285
windows-devel	NOTE	328
windows-release	NOTE	358
windows-oldrel	NOTE	331
wasm-release	OK	198

Exports:cexor plotcexor pskellam pskellam.sp

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops BSgenome cigarillo cli clipr codetools cpp11 crayon curl data.table DelayedArray farver formatR futile.logger futile.options generics genomation GenomicAlignments GenomicRanges ggplot2 glue gridBase gtable hms httr idr impute IRanges isoband jsonlite KernSmooth labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig plotrix plyr prettyunits progress R6 RColorBrewer Rcpp RCurl readr reshape2 restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors S7 scales Seqinfo seqPattern snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyselect tzdb utf8 vctrs viridisLite vroom withr XML XVector yaml

CexoR Vignette

Rendered fromCexoR.Rnwusingutils::Sweave

Last update: 2022-05-28
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates	CexoR-package CexoR
ChIP-exo peak-pair calling with replicates	cexor
Visualization of ChIP-exo peak-pair calling with replicates	plotcexor