R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 11 found.
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binom.test.REDseq (Package: REDseq) :

For any early stage experiment with one experimental condition and one biological replicate, binom.test.REDseq computes p-value for each RE site in the genome.

● Data Source: BioConductor
● Keywords: Statistics
● Alias: binom.test.REDseq
● 0 images

buildREmap (Package: REDseq) :

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

● Data Source: BioConductor
● Keywords: misc
● Alias: buildREmap
● 0 images

compareREDseq (Package: REDseq) :

For early stage experiment without replicates, compareREDseq outputs differentially cut RE sites between two experimental conditions using Fisher's Exact Test.

● Data Source: BioConductor
● Keywords: Statistics
● Alias: compareREDseq
● 0 images

distanceHistSeq2RE (Package: REDseq) :

Give an overview of the distance distribution from all assigned sequences to the associated RE sites. If average or estimate is used for assigning sequences to RE sites, the count for histogram drawing will be adjusted with the weight assigned.

● Data Source: BioConductor
● Keywords: graph
● Alias: distanceHistSeq2RE
● 2 images

plotCutDistribution (Package: REDseq) :

plot cut frequencies of RE sites along a chromosome, which gives a bird-eye view of genome-wide frequent-cut regions and RE inaccessible regions.

● Data Source: BioConductor
● Keywords: graph
● Alias: plotCutDistribution
● 1 images

searchPattern (Package: REDseq) :

internal function for searching pattern(s) in a genome used by buildREmap leveraging BSgenome package

● Data Source: BioConductor
● Keywords: internal
● Alias: searchPattern
● 0 images

summarizeByRE (Package: REDseq) :

Output count/weight summary by REid with each row representing each REid

● Data Source: BioConductor
● Keywords: misc
● Alias: summarizeByRE
● 0 images

summarizeBySeq (Package: REDseq) :

Output count/weight summary by sequences with each row representing each sequences

● Data Source: BioConductor
● Keywords: misc
● Alias: summarizeBySeq
● 0 images

writeHits (Package: REDseq) :

write the hits of pattern search to a bed file, internal function used by searchPattern

● Data Source: BioConductor
● Keywords: internal
● Alias: writeHits
● 0 images

REDseq-package (Package: REDseq) :

REDSeq is a Bioconductor package for building genomic map of restriction enzyme sites REmap, assigning sequencing tags to RE sites using five different strategies, visualizing genome-wide distribution of differentially cut regions with the REmap as reference and the distance distribution of sequence tags to corresponding RE sites, generating count table for identifying statistically significant RE sites using edgeR or DEseq.

● Data Source: BioConductor
● Keywords: package
● Alias: REDseq, REDseq-package
● 3 images