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

Functions

addBamData Man page
addDataToReadset Man page
addExperimentsToReadset Man page
allCamelMeasuresForRegion Man page
averageND Man page
bam2sig Man page
buildDESeq Man page
buildDGEList Man page
combineND Man page
densityNormalize Man page
diff_area Man page
diff_derivative_area Man page
distrCOVPlot Man page
distrCOVPlotg Man page
distribs Man page
distrSIPlot Man page
findRegionsAsIR Man page
findRegionsAsND Man page
fiveCol2GRanges Man page
gcoverage Man page
geneInChromosome Man page
generatorAdd Man page
generatorAddSquare Man page
generatorMultiply Man page
generatorPeak Man page
generatorSynth Man page
generatorTrunc Man page
getBamData Man page
getCoverageFromRS Man page
getData Man page
getDistr Man page
getExpDescription Man page
getFCFromND Man page
getSIFromND Man page
getSumsExp Man page
ghistogram Man page
globalCountsNormalize Man page
gRanges2CamelMeasures Man page
hump_diff1 Man page
hump_diff2 Man page
ks_test Man page
log2ND Man page
min_maxNormalize Man page
newNuctleotideDistr Man page
newSeqReads Man page
newSeqReadsFromGene Man page
normalizeBySum Man page
NucleotideDistr-class Man page
parseGff3 Man page
plotCoverageHistogram Man page
plotExonCoverage Man page
plotGeneCoverage Man page
plotGeneExonCoverage Man page
plotRegionCoverage Man page
plotSI Man page
pp_derivative_plot Man page
pp_plot Man page
qq_derivative_plot Man page
qq_plot Man page
readsInRange Man page
regionBasedCoverage Man page
regionCoverage Man page
regionmining Man page
RleList2matrix Man page
rs.list Man page
sample_data_rnaSeqMap Man page
SeqReads Man page
SeqReads-class Man page
setData Man page
setSAXPYData Man page
setSpecies Man page
simplePlot Man page
spaceInChromosome Man page
splicingind Man page
standarizationNormalize Man page
sumND Man page

Files

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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