Package: recoup 1.41.0

Panagiotis Moulos

recoup: An R package for the creation of complex genomic profile plots

recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.

Authors:Panagiotis Moulos <[email protected]>

recoup_1.41.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
recoup/json (API)

# Install 'recoup' in R:

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

Bug tracker:https://github.com/pmoulos/recoup/issues

Datasets:

test.design - Reference and genomic sample regions for recoup testing
test.exons - Reference and genomic sample regions for recoup testing
test.genome - Reference and genomic sample regions for recoup testing
test.input - Reference and genomic sample regions for recoup testing

On BioConductor:recoup-1.41.0(bioc 3.24)recoup-1.40.0(bioc 3.23)

immunooncology software geneexpression preprocessing qualitycontrol rnaseq chipseq sequencing coverage atacseq chiponchip alignment dataimport

5.24 score 1 stars 7 scripts 1 mentions 24 exports 112 dependencies

Last updated from:ad7ae07e1e. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	211
linux-devel-x86_64	NOTE	544
source / vignettes	OK	352
linux-release-x86_64	NOTE	488
macos-release-arm64	NOTE	277
macos-oldrel-arm64	NOTE	260
windows-devel	NOTE	540
windows-release	NOTE	429
windows-oldrel	NOTE	596
wasm-release	OK	157

Exports:buildAnnotationDatabase buildCustomAnnotation calcCoverage coverageRef coverageRnaRef getAnnotation getBiotypes getInstalledAnnotations getr importCustomAnnotation kmeansDesign loadAnnotation mergeRuns preprocessRanges profileMatrix recoup recoupCorrelation recoupHeatmap recoupPlot recoupProfile removeData rpMatrix setr sliceObj

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cigarillo circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl DBI dbplyr DelayedArray digest doParallel dplyr farver fastmap filelock foreach formatR futile.logger futile.options generics GenomeInfoDb GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggplot2 GlobalOptions glue gtable hms httr httr2 IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png prettyunits progress purrr R6 rappdirs RColorBrewer RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors S7 scales Seqinfo shape snow SparseArray stringi stringr SummarizedExperiment sys tibble tidyr tidyselect txdbmaker UCSC.utils utf8 vctrs viridisLite withr XML xml2 XVector yaml

Usage of the recoup package

Rendered fromrecoup_intro.Rmdusingknitr::rmarkdown

Last update: 2020-05-04
Started: 2016-03-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Build a local annotation database for recoup	buildAnnotationDatabase
Import custom annotation to the recoup annotation database from GTF file	buildCustomAnnotation
Calculate coverages over a genomic region	calcCoverage
Calculate coverage in a set of reference genomic regions (ChIP-Seq or unspliced mode)	coverageRef
Calculate coverage in a set of reference genomic regions (RNA-Seq or spliced mode)	coverageRnaRef
Annotation downloader	getAnnotation
List default Ensembl biotypes	getBiotypes
Load a recoup annotation element	getInstalledAnnotations
Import a recoup custom annotation element	importCustomAnnotation
Apply k-means clustering to profile data	kmeansDesign
Load a recoup annotation element	loadAnnotation
Merge recoup outputs of same type	mergeRuns
Read and preprocess BAM/BED files to GRanges	preprocessRanges
Calculate final profile matrices for plotting	profileMatrix
Create genomic signal profiles in predefined or custom areas using short sequence reads	recoup
Reference and genomic sample regions for recoup testing	recoup_test_data test.design test.exons test.genome test.input
Plot (faceted) average genomic coverage correlations	recoupCorrelation
Plot genomic coverage heatmaps	recoupHeatmap
Plot list objects returned by recoup	recoupPlot
Plot (faceted) average genomic coverage profiles	recoupProfile
Remove data from recoup list object	removeData
Reads per million profile matrices for plotting	rpMatrix
Get and set some reusable objects from a recoup object	getr setr
Subset recoup output list objects	sliceObj