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.

Author
Lihua Julie Zhu and Thomas Fazzio
Date of publication
None
Maintainer
Lihua Julie Zhu <julie.zhu@umassmed.edu>
License
GPL (>=2)
Version
1.20.0

View on Bioconductor

Man pages

assignSeq2REsite
Assign mapped sequence tags to corresponding restriction...
binom.test.REDseq
Binomial test for REDseq dataset
buildREmap
Build a genome wide cut site map for a Restriction Enzyme...
compareREDseq
Compare two RED Sequencing Dataset
distanceHistSeq2RE
Plot the distance distribution from sequence to the...
example.assignedREDseq
an example assigned REDseq dataset
example.map
an example REmap dataset
example.REDseq
an example sequencing dataset from a restoration enzyme...
plotCutDistribution
plot cut frequencies of RE sites along a given chromosome
REDseq-package
REDseq
searchPattern
search pattern(s) in a genome
summarizeByRE
Output count/weight summary by restriction enzyme cut site ID...
summarizeBySeq
Output count/weight summary by sequences
writeHits
write the hits of pattern search to a bed file

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