rnaSeqMap: rnaSeq secondary analyses

The rnaSeqMap library provides classes and functions to analyze the RNA-sequencing data using the coverage profiles in multiple samples at a time

AuthorAnna Lesniewska <alesniewska@cs.put.poznan.pl>; Michal Okoniewski <michal@fgcz.ethz.ch>
Date of publicationNone
MaintainerMichal Okoniewski <michal@fgcz.ethz.ch>
LicenseGPL-2
Version2.32.0

View on Bioconductor

Man pages

addBamData: addBamData - getting sample data from BAM file.

addDataToReadset: addDataToReadset - adding one more sample in the SeqRead on R...

addExperimentsToReadset: addExperimentsToReadset - getting sample data from the...

averageND: averageND, sumND, combineNS, log2ND - operations on...

bam2sig: bam2sig - encapsulated pipeline of finding significant...

buildDESeq: buildDESeq - create CountDataSet

buildDGEList: buildDGEList - create DGEList (edgeR)

findRegionsAsIR: findRegionsAsIR - finding regions of high coverage using...

findRegionsAsND: findRegionsAsND - finding regions of high coverage using...

fiveCol2GRanges: fiveCol2GRanges

geneInChromosome: geneInChromosome

generators: Generators for synt data and

getBamData: getBamData - getting sample data from BAM file.

getCoverageFromRS: getCoverageFromRS - conversion to coverage object

getData: Data accessor function for rnaSeqMap objects containing...

getExpDescription: getExpDescription

getFCFromND: getFCFromND - calculating fold change of coverages

getSIFromND: getSIFromND - calculating splicing index of two coverages

getSumsExp: getSumsExp

gRanges2CamelMeasures: Genomic plots based upon NucleotideDistr objects

measures: Measures

NDplots: Genomic plots based upon NucleotideDistr objects

normalizations: Normalization Methods

normalizeBySum: Normalization of NucleotideDistr by global number of reads

NucleotideDistr-class: Numeric distributions by nucleotide - class

parseGff3: parseGff3 - parsing gff3 file format

plotGeneCoverage: Genomic plots with rnaSeqMap

readsInRange: readsInRange

regionBasedCoverage: regionBasedCoverage - transformation of the region coverage...

regionCoverage: regionCoverage

RleList2matrix: RleList2matrix

rs.list: Example of sequencing data for rnaSeqMap library

SeqReds: SeqReads - a container for RNAseq reads

setData: Data accessor function for rnaSeqMap objects containing...

setSAXPYData: Data accessor function for rnaSeqMap objects containing...

setSpecies: setSpecies

simplePlot: simplePlot - quick plot for the coverages

spaceInChromosome: spaceInChromosome

Files in this package

rnaSeqMap/DESCRIPTION
rnaSeqMap/NAMESPACE
rnaSeqMap/R
rnaSeqMap/R/NDplots.R rnaSeqMap/R/NDtransforms.R rnaSeqMap/R/NucleotideDistr.R rnaSeqMap/R/SeqReads.R rnaSeqMap/R/bam2sig.R rnaSeqMap/R/camelWrapper.R rnaSeqMap/R/generators.R rnaSeqMap/R/measures.R rnaSeqMap/R/normalizations.R rnaSeqMap/R/parseGff3.R rnaSeqMap/R/pipelines.R rnaSeqMap/R/plots.R rnaSeqMap/R/utils.R rnaSeqMap/R/zzz.R
rnaSeqMap/build
rnaSeqMap/build/vignette.rds
rnaSeqMap/data
rnaSeqMap/data/sample_data_rnaSeqMap.RData
rnaSeqMap/inst
rnaSeqMap/inst/doc
rnaSeqMap/inst/doc/rnaSeqMap.R
rnaSeqMap/inst/doc/rnaSeqMap.Rnw
rnaSeqMap/inst/doc/rnaSeqMap.pdf
rnaSeqMap/inst/extdata
rnaSeqMap/inst/scripts
rnaSeqMap/inst/scripts/README_SQL
rnaSeqMap/inst/scripts/bio_sample.sql
rnaSeqMap/inst/scripts/importdb.bat
rnaSeqMap/inst/scripts/importdb.sh
rnaSeqMap/inst/scripts/indices.sql
rnaSeqMap/inst/scripts/procedures.sql
rnaSeqMap/inst/scripts/rnaSeqMap.sql
rnaSeqMap/inst/scripts/seq_read.sql
rnaSeqMap/man
rnaSeqMap/man/NDplots.Rd rnaSeqMap/man/NucleotideDistr-class.Rd rnaSeqMap/man/RleList2matrix.Rd rnaSeqMap/man/SeqReds.Rd rnaSeqMap/man/addBamData.Rd rnaSeqMap/man/addDataToReadset.Rd rnaSeqMap/man/addExperimentsToReadset.Rd rnaSeqMap/man/averageND.Rd rnaSeqMap/man/bam2sig.Rd rnaSeqMap/man/buildDESeq.Rd rnaSeqMap/man/buildDGEList.Rd rnaSeqMap/man/findRegionsAsIR.Rd rnaSeqMap/man/findRegionsAsND.Rd rnaSeqMap/man/fiveCol2GRanges.Rd rnaSeqMap/man/gRanges2CamelMeasures.Rd rnaSeqMap/man/geneInChromosome.Rd rnaSeqMap/man/generators.Rd rnaSeqMap/man/getBamData.Rd rnaSeqMap/man/getCoverageFromRS.Rd rnaSeqMap/man/getData.Rd rnaSeqMap/man/getExpDescription.Rd rnaSeqMap/man/getFCFromND.Rd rnaSeqMap/man/getSIFromND.Rd rnaSeqMap/man/getSumsExp.Rd rnaSeqMap/man/measures.Rd rnaSeqMap/man/normalizations.Rd rnaSeqMap/man/normalizeBySum.Rd rnaSeqMap/man/parseGff3.Rd rnaSeqMap/man/plotGeneCoverage.Rd rnaSeqMap/man/readsInRange.Rd rnaSeqMap/man/regionBasedCoverage.Rd rnaSeqMap/man/regionCoverage.Rd rnaSeqMap/man/rs.list.Rd rnaSeqMap/man/setData.Rd rnaSeqMap/man/setSAXPYData.Rd rnaSeqMap/man/setSpecies.Rd rnaSeqMap/man/simplePlot.Rd rnaSeqMap/man/spaceInChromosome.Rd
rnaSeqMap/src
rnaSeqMap/src/Rinit.c
rnaSeqMap/src/gcoverage.c
rnaSeqMap/src/ghistogram.c
rnaSeqMap/src/regionmining.c
rnaSeqMap/src/splicingind.c
rnaSeqMap/vignettes
rnaSeqMap/vignettes/rnaSeqMap.Rnw
rnaSeqMap/vignettes/rnaSeqMap_with_db.Rnw.gz
rnaSeqMap/vignettes/rnaSeqMap_with_db.pdf.gz

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