Package: recoup 1.33.0

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]>

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recoup.pdf |recoup.html✨
recoup/json (API)
NEWS

# 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-1.33.0(bioc 3.20)recoup-1.32.0(bioc 3.19)

bioconductor-package

25 exports 1.16 score 116 dependencies 1 mentions

Last updated 2 months agofrom:351206b864

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

Usage of the recoup package

Panagiotis Moulos

Rendered fromrecoup_intro.Rmdusingknitr::rmarkdownon Jun 25 2024.

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
Build a local annotation database for recoup	buildAnnotationStore
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
Defunct functions in package 'recoup'	recoup-defunct
Deprecated functions in package 'recoup'	recoup-deprecated
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