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REDseq (version 1.18.0)

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

Description

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.

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Version

Version

1.18.0

License

GPL (>=2)

Maintainer

Lihua Julie Zhu

Last Published

February 15th, 2017

Functions in REDseq (1.18.0)

example.REDseq

an example sequencing dataset from a restoration enzyme digestion (RED) experiment
searchPattern

search pattern(s) in a genome
summarizeByRE

Output count/weight summary by restriction enzyme cut site ID (REid)
example.assignedREDseq

an example assigned REDseq dataset
REDseq-package

REDseq
assignSeq2REsite

Assign mapped sequence tags to corresponding restriction enzyme (RE) cut sites
example.map

an example REmap dataset
distanceHistSeq2RE

Plot the distance distribution from sequence to the associated RE sites
buildREmap

Build a genome wide cut site map for a Restriction Enzyme (RE)
writeHits

write the hits of pattern search to a bed file
plotCutDistribution

plot cut frequencies of RE sites along a given chromosome
binom.test.REDseq

Binomial test for REDseq dataset
summarizeBySeq

Output count/weight summary by sequences
compareREDseq

Compare two RED Sequencing Dataset