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.

AuthorLihua Julie Zhu and Thomas Fazzio
Date of publicationNone
MaintainerLihua Julie Zhu <julie.zhu@umassmed.edu>
LicenseGPL (>=2)
Version1.20.0

View on Bioconductor

Files in this package

REDseq/DESCRIPTION
REDseq/NAMESPACE
REDseq/R
REDseq/R/assignSeq2REsite.R REDseq/R/binom.test.REDseq.R REDseq/R/buildREmap.R REDseq/R/compareREDseq.R REDseq/R/distanceHistSeq2RE.R REDseq/R/plotCutDistribution.R REDseq/R/searchPattern.R REDseq/R/summarizeByRE.R REDseq/R/summarizeBySeq.R REDseq/R/writeHits.R
REDseq/build
REDseq/build/vignette.rds
REDseq/data
REDseq/data/example.REDseq.rda
REDseq/data/example.assignedREDseq.rda
REDseq/data/example.map.rda
REDseq/inst
REDseq/inst/doc
REDseq/inst/doc/REDseq.R
REDseq/inst/doc/REDseq.Rnw
REDseq/inst/doc/REDseq.pdf
REDseq/inst/extdata
REDseq/inst/extdata/REsitesUnique.fasta
REDseq/inst/extdata/TSS1kbCutFreqAndVariance_hg19.xls
REDseq/inst/extdata/TSS1kbCutFreqAndVariance_mm9.xls
REDseq/inst/extdata/examplePattern.fa
REDseq/man
REDseq/man/REDseq-package.Rd REDseq/man/assignSeq2REsite.Rd REDseq/man/binom.test.REDseq.Rd REDseq/man/buildREmap.Rd REDseq/man/compareREDseq.Rd REDseq/man/distanceHistSeq2RE.Rd REDseq/man/example.REDseq.Rd REDseq/man/example.assignedREDseq.Rd REDseq/man/example.map.Rd REDseq/man/plotCutDistribution.Rd REDseq/man/searchPattern.Rd REDseq/man/summarizeByRE.Rd REDseq/man/summarizeBySeq.Rd REDseq/man/writeHits.Rd
REDseq/vignettes
REDseq/vignettes/REDseq.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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