Package: DEScan2 1.33.0

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]

DEScan2_1.33.0.tar.gz
DEScan2_1.33.0.zip(r-4.7)DEScan2_1.33.0.zip(r-4.6)DEScan2_1.31.0.zip(r-4.5)
DEScan2_1.33.0.tgz(r-4.6-x86_64)DEScan2_1.33.0.tgz(r-4.6-arm64)DEScan2_1.31.0.tgz(r-4.5-x86_64)DEScan2_1.31.0.tgz(r-4.5-arm64)
DEScan2_1.33.0.tar.gz(r-4.7-arm64)DEScan2_1.33.0.tar.gz(r-4.7-x86_64)DEScan2_1.33.0.tar.gz(r-4.6-arm64)DEScan2_1.33.0.tar.gz(r-4.6-x86_64)
DEScan2_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DEScan2/json (API)

# 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:DEScan2-1.33.0(bioc 3.24)DEScan2-1.32.0(bioc 3.23)

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 cpp

3.48 score 4 scripts 1 mentions 18 exports 120 dependencies

Last updated from:47c99148d9. Checks:1 ERROR, 8 NOTE, 2 OK, 3 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	248
linux-devel-arm64	NOTE	428
linux-devel-x86_64	NOTE	553
source / vignettes	OK	371
linux-release-arm64	NOTE	439
linux-release-x86_64	NOTE	539
macos-release-arm64	NOTE	317
macos-release-x86_64	NOTE	651
macos-oldrel-arm64	FAIL	68
macos-oldrel-x86_64	FAIL	154
windows-devel	NOTE	546
windows-release	NOTE	499
windows-oldrel	FAIL	108
wasm-release	OK	217

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 BiocBaseUtils BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome cachem ChIPpeakAnno cigarillo cli codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray dplyr ensembldb farver fastmap filelock formatR futile.logger futile.options generics GenomeInfoDb 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 mime multtest openssl pillar pkgconfig 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 S7 scales Seqinfo snow SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils universalmotif utf8 vctrs VennDiagram viridisLite withr XML xml2 XVector yaml

DEScan2

Overview | A typical differential enrichment analysis workflow | A note on performance and serial computing

Rendered fromDEScan2.Rmdusingknitr::rmarkdown

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