Package: DEScan2 1.27.0

Dario Righelli

DEScan2: Differential Enrichment Scan 2

Integrated peak and differential caller, specifically designed for broad epigenomic signals.

Authors:Dario Righelli [aut, cre], John Koberstein [aut], Bruce Gomes [aut], Nancy Zhang [aut], Claudia Angelini [aut], Lucia Peixoto [aut], Davide Risso [aut]

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DEScan2.pdf |DEScan2.html✨
DEScan2/json (API)
NEWS

# Install 'DEScan2' in R:

install.packages('DEScan2', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:DEScan2-1.25.0(bioc 3.20)DEScan2-1.24.0(bioc 3.19)

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

immunooncology peakdetection epigenetics software sequencing coverage

3.30 score 2 scripts 207 downloads 18 exports 125 dependencies

Last updated 23 days agofrom:b34d6d07e9. Checks:OK: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win-x86_64	WARNING	Oct 30 2024
R-4.5-linux-x86_64	WARNING	Oct 30 2024
R-4.4-win-x86_64	WARNING	Oct 30 2024
R-4.4-mac-x86_64	WARNING	Oct 30 2024
R-4.4-mac-aarch64	WARNING	Oct 30 2024
R-4.3-win-x86_64	WARNING	Oct 30 2024
R-4.3-mac-x86_64	WARNING	Oct 30 2024
R-4.3-mac-aarch64	WARNING	Oct 30 2024

Exports:binnedCoverage constructBedRanges countFinalRegions createGranges cutGRangesPerChromosome divideEachSampleByChromosomes finalRegions findOverlapsOverSamples findPeaks fromSamplesToChrsGRangesList keepRelevantChrs readBamAsBed readBedFile readFilesAsGRangesList RleListToRleMatrix saveGRangesAsBed saveGRangesAsTsv setGRGenomeInfo

Dependencies:abind AnnotationDbi AnnotationFilter askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome cachem ChIPpeakAnno cli codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray digest dplyr ensembldb fansi farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue graph gtable hms httr httr2 InteractionSet IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime multtest munsell nlme openssl pillar pkgconfig plogr plyr png prettyunits progress ProtGenerics purrr pwalign R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RcppThread RCurl regioneR restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales snow SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils universalmotif utf8 vctrs VennDiagram viridisLite withr XML xml2 XVector yaml zlibbioc

DEScan2

Dario Righelli - John Koberstein - Bruce Gomes

Rendered fromDEScan2.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2019-02-26
Started: 2017-12-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
binnedCoverage	binnedCoverage
computeZ	computeZ
constructBedRanges	constructBedRanges
countFinalRegions	countFinalRegions
createGranges	createGranges
cutGRangesPerChromosome	cutGRangesPerChromosome
DEScan2	DEScan2
divideEachSampleByChromosomes	divideEachSampleByChromosomes
finalRegions	finalRegions
findOverlapsOverSamples	findOverlapsOverSamples
findPeaks	findPeaks
fromSamplesToChrsGRangesList	fromSamplesToChrsGRangesList
keepRelevantChrs	keepRelevantChrs
readBamAsBed	readBamAsBed
readBedFile	readBedFile
readFilesAsGRangesList	readFilesAsGRangesList
RleListToRleMatrix	RleListToRleMatrix
saveGRangesAsBed	saveGRangesAsBed
saveGRangesAsTsv	saveGRangesAsTsv
setGRGenomeInfo given a genome code (i.e. "mm9","mm10","hg19","hg38") retrieve the SeqInfo of that genome and assigns it to the input GRanges. Finally filters out those Infos not necessary to the GRanges.	setGRGenomeInfo