Package: REDseq 1.53.0

Lihua Julie Zhu

REDseq: Analysis of high-throughput sequencing data processed by restriction enzyme digestion

The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.

Authors:Lihua Julie Zhu, Junhui Li and Thomas Fazzio

REDseq_1.53.0.tar.gz
REDseq_1.53.0.zip(r-4.5)REDseq_1.53.0.zip(r-4.4)REDseq_1.53.0.zip(r-4.3)
REDseq_1.53.0.tgz(r-4.5-any)REDseq_1.53.0.tgz(r-4.4-any)REDseq_1.53.0.tgz(r-4.3-any)
REDseq_1.53.0.tar.gz(r-4.5-noble)REDseq_1.53.0.tar.gz(r-4.4-noble)
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REDseq.pdf |REDseq.html
REDseq/json (API)

# Install 'REDseq' in R:
install.packages('REDseq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On BioConductor:REDseq-1.53.0(bioc 3.21)REDseq-1.52.0(bioc 3.20)

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

sequencingsequencematchingpreprocessing

3.48 score 15 scripts 328 downloads 1 mentions 8 exports 123 dependencies

Last updated 5 months agofrom:c53b524b48. Checks:1 OK, 8 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 30 2025
R-4.5-winNOTEMar 30 2025
R-4.5-macNOTEMar 30 2025
R-4.5-linuxNOTEMar 30 2025
R-4.4-winNOTEMar 30 2025
R-4.4-macNOTEMar 30 2025
R-4.4-linuxNOTEMar 30 2025
R-4.3-winNOTEMar 30 2025
R-4.3-macNOTEMar 30 2025

Exports:assignSeq2REsitebinom.test.REDseqbuildREmapcompareREDseqdistanceHistSeq2REplotCutDistributionsummarizeByREsummarizeBySeq

Dependencies:abindAnnotationDbiAnnotationFilteraskpassBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobBSgenomeBSgenome.Celegans.UCSC.ce2cachemChIPpeakAnnoclicodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydigestdplyrensembldbfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegraphgtablehmshttrhttr2InteractionSetIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemulttestmunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogressProtGenericspurrrpwalignR6rappdirsRBGLRColorBrewerRcppRcppThreadRCurlregioneRrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsuniversalmotifutf8vctrsVennDiagramviridisLitewithrXMLxml2XVectoryaml

REDseq Vignette

Rendered fromREDseq.Rnwusingutils::Sweaveon Mar 30 2025.

Last update: 2021-03-10
Started: 2013-10-21