Package: ChIPexoQual 1.29.0

Rene Welch

ChIPexoQual: ChIPexoQual

Package with a quality control pipeline for ChIP-exo/nexus data.

Authors:Rene Welch, Dongjun Chung, Sunduz Keles

ChIPexoQual_1.29.0.tar.gz
ChIPexoQual_1.29.0.zip(r-4.5)ChIPexoQual_1.29.0.zip(r-4.4)ChIPexoQual_1.29.0.zip(r-4.3)
ChIPexoQual_1.29.0.tgz(r-4.4-any)ChIPexoQual_1.29.0.tgz(r-4.3-any)
ChIPexoQual_1.29.0.tar.gz(r-4.5-noble)ChIPexoQual_1.29.0.tar.gz(r-4.4-noble)
ChIPexoQual_1.29.0.tgz(r-4.4-emscripten)ChIPexoQual_1.29.0.tgz(r-4.3-emscripten)
ChIPexoQual.pdf |ChIPexoQual.html✨
ChIPexoQual/json (API)
NEWS

# Install 'ChIPexoQual' in R:

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

Bug tracker:https://github.com/welch16/chipexoqual/issues

Datasets:

blacklists - 'list' of 'GRanges' objects with the blacklists generated by the ENCODE and modENCODE projects.
exoExample - 'ExoData' results for FoxA1 ChIP-exo experiment

On BioConductor:ChIPexoQual-1.29.0(bioc 3.20)ChIPexoQual-1.28.0(bioc 3.19)

bioconductor-package

14 exports 0.91 score 133 dependencies 1 mentions

Last updated 2 months agofrom:22bd18aef4

Exports:ARCvURCplot beta1 beta2 calculateParamDist ExoData ExoDataBlacklist ExoDataSubsampling formatRegions FSRDistplot MAplot nreads paramDist paramDistBoxplot regionCompplot

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings biovizBase bit bit64 bitops blob broom BSgenome bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI DelayedArray dichromat digest dplyr ensembldb evaluate fansi farver fastmap fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable hexbin highr Hmisc htmlTable htmltools htmlwidgets httr IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr png ProtGenerics purrr R6 rappdirs RColorBrewer RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML XVector yaml zlibbioc

ChIPexoQual: A quality control pipeline for ChIP-exo/nexus data.

| Rene Welch and Sündüz Keleş | Department of Statistics, University of Wisconsin-Madison

Rendered fromvignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2018-01-24
Started: 2016-07-18

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
ARCvURCplot	ARCvURCplot
beta1 methods	beta1 beta1,ExoData-method
beta2 methods	beta2 beta2,ExoData-method
'list' of 'GRanges' objects with the blacklists generated by the ENCODE and modENCODE projects.	blacklists
calculateParamDist 'calculateParamDist' calculates the quality parameters of one iteration. This function samples 'nregions' rows from the stat matrix and fits the linear model 'lm(d ~ 0 + u + w)'	calculateParamDist
ExoData object and constructors	ExoData ExoData-class
ExoDataBlacklist	ExoDataBlacklist
ExoDataSubsampling	ExoDataSubsampling
'ExoData' results for FoxA1 ChIP-exo experiment	exoExample
formatRegions 'formatRegions' separates the width, depth and uniquePos summary statistics from the 'ExoData' object to calculate the quality parameters/	formatRegions
FSRDistplot	FSRDistplot
MAplot	MAplot
nreads methods	nreads nreads,ExoData-method
paramDist methods	paramDist paramDist,ExoData-method
paramDistBoxplot	paramDistBoxplot
regionCompplot	regionCompplot

Usage by other packages (reverse dependencies)