rnaSeqMap: rnaSeq secondary analyses

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

Author
Anna Lesniewska <alesniewska@cs.put.poznan.pl>; Michal Okoniewski <michal@fgcz.ethz.ch>
Date of publication
None
Maintainer
Michal Okoniewski <michal@fgcz.ethz.ch>
License
GPL-2
Version
2.32.0

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