spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

Performs splice centered analysis on RNA-seq data.

AuthorWolfgang Kaisers
Date of publicationNone
MaintainerWolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
LicenseGPL-2
Version1.22.0

View on Bioconductor

Man pages

aaGapSites-class: Class '"aaGapSites"'

addGeneAligns: Reads a bamRange object for a given 'bamReader', 'refGenome'...

addHbond: Class '"hbond"': Provides data and functions for calculation...

addMaxEnt: addMaxEnt: Extract subset of data contained in given range...

alt_X_ranks: alt_left_ranks and alt_right_ranks functions: Identification...

annGapSites-class: Class '"annGapSites"'

annotate-ExpressionSet: Adds annotation data to existing ExpressionSet (created by...

annotation: Annotation functions for 'gapSites' objects

as.data.frame-methods: 'as.data.frame' Returning content of data.frame.

caRanges-class: Class '"caRanges"'

cdRanges-class: Class '"cdRanges"'

c-methods: Coercing functions 'c'.

countByGeneName: Reads align number for selected gene from multiple BAM-files.

cRanges-class: Class '"cRanges"': Centered ranges.

dim-methods: 'dim': Return dimensions of contained data.frame.

dnaGapSites-class: Class '"dnaGapSites"'

dnaRanges: Reads a bamRange object for a given 'bamReader', 'refGenome'...

extractByGeneName: extractByGeneName: Extract subset for sites which lie in...

extractRange: extractRange: Extract subset from object where records lie in...

gapSites: Creating 'gapSites' and 'dnaGapSites' objects.

gapSites-class: Class '"gapSites"': Container for tabulated alignment gap...

getGapSites: Read 'gapSites'

hbond-class: Class '"hbond"'

head-methods: 'head' Return first lines of contained data.frame.

initialize-methods: 'initialize' Initializing objects.

keyProfiler-class: Class '"keyProfiler"'

lrCodons: lrCodon methods

maxEnt-class: Class '"maxEnt"'

merge-methods: 'merge' Merging two objects into one.

plotGeneAlignDepth: plotGeneAlignDepth: Plots of read alignment depth for genetic...

rangeByGeneName: Reads a bamRange object for a given 'bamReader', 'refGenome'...

readCuffGeneFpkm: Reads FPKM values into ExpressionSet.

readExpSet: Reads align number or gptm or rpmg value from all given...

readMergedBamGaps: Reads an object of type 'gapSites' using a vector of BAM file...

readTabledBamGaps: readTabledBamGaps function

seqlogo: seqlogo: Plotting sequence logo for 'cdRanges' and...

silic_tryp: silic_tryp function

sortTable-methods: Sorting contained data with 'sortTable'.

SpliceCountSet-class: Class '"SpliceCountSet"'

spliceSites-package: Calculate information on splice-sites from gapped alignments...

trim: trim and resize methods: trim_left, trim_right, resize_left,...

truncate_seq: truncate_seq function

truncateSeq: truncateSeq method

trypsinCleave: trypsinCleave method

uniqueJuncAnn: uniqueJuncAnn method for ExpressionSet

write.files: write.files

xCodons: xCodon methods

xJunc: xJunc methods: lJunc, rJunc, lrJunc

xJuncStrand: xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand

z[-methods: Methods for Function '['.

Files in this package

spliceSites/ChangeLog
spliceSites/DESCRIPTION
spliceSites/NAMESPACE
spliceSites/NEWS
spliceSites/R
spliceSites/R/allClasses.r
spliceSites/R/allGenerics.r
spliceSites/R/c-methods.r
spliceSites/R/dim-methods.r
spliceSites/R/head-methods.r
spliceSites/R/show-methods.r
spliceSites/R/spliceSites.r
spliceSites/build
spliceSites/build/vignette.rds
spliceSites/inst
spliceSites/inst/doc
spliceSites/inst/doc/spliceSites.R
spliceSites/inst/doc/spliceSites.Rnw
spliceSites/inst/doc/spliceSites.pdf
spliceSites/inst/extdata
spliceSites/inst/extdata/cuff_files
spliceSites/inst/extdata/cuff_files/1.genes.fpkm_tracking
spliceSites/inst/extdata/cuff_files/10.genes.fpkm_tracking
spliceSites/inst/extdata/cuff_files/2.genes.fpkm_tracking
spliceSites/inst/extdata/cuff_files/3.genes.fpkm_tracking
spliceSites/inst/extdata/cuff_files/4.genes.fpkm_tracking
spliceSites/inst/extdata/cuff_files/5.genes.fpkm_tracking
spliceSites/inst/extdata/cuff_files/6.genes.fpkm_tracking
spliceSites/inst/extdata/cuff_files/7.genes.fpkm_tracking
spliceSites/inst/extdata/cuff_files/8.genes.fpkm_tracking
spliceSites/inst/extdata/cuff_files/9.genes.fpkm_tracking
spliceSites/inst/extdata/cuff_files/groups.csv
spliceSites/inst/extdata/dna_small.RData
spliceSites/inst/extdata/ens_small.RData
spliceSites/inst/extdata/hbs.RData
spliceSites/inst/extdata/key.RData
spliceSites/inst/extdata/maxent.RData
spliceSites/inst/extdata/rna_fem.bam
spliceSites/inst/extdata/rna_fem.bam.bai
spliceSites/inst/extdata/rna_mal.bam
spliceSites/inst/extdata/rna_mal.bam.bai
spliceSites/inst/extdata/uc_small.RData
spliceSites/inst/extdata/uc_small_junc.RData
spliceSites/man
spliceSites/man/SpliceCountSet-class.Rd spliceSites/man/aaGapSites-class.Rd spliceSites/man/addGeneAligns.Rd spliceSites/man/addHbond.Rd spliceSites/man/addMaxEnt.Rd spliceSites/man/alt_X_ranks.Rd spliceSites/man/annGapSites-class.Rd spliceSites/man/annotate-ExpressionSet.Rd spliceSites/man/annotation.Rd spliceSites/man/as.data.frame-methods.Rd spliceSites/man/c-methods.Rd spliceSites/man/cRanges-class.Rd spliceSites/man/caRanges-class.Rd spliceSites/man/cdRanges-class.Rd spliceSites/man/countByGeneName.Rd spliceSites/man/dim-methods.Rd spliceSites/man/dnaGapSites-class.Rd spliceSites/man/dnaRanges.Rd spliceSites/man/extractByGeneName.Rd spliceSites/man/extractRange.Rd spliceSites/man/gapSites-class.Rd spliceSites/man/gapSites.Rd spliceSites/man/getGapSites.Rd spliceSites/man/hbond-class.Rd spliceSites/man/head-methods.Rd spliceSites/man/initialize-methods.Rd spliceSites/man/keyProfiler-class.Rd spliceSites/man/lrCodons.Rd spliceSites/man/maxEnt-class.Rd spliceSites/man/merge-methods.Rd spliceSites/man/plotGeneAlignDepth.Rd spliceSites/man/rangeByGeneName.Rd spliceSites/man/readCuffGeneFpkm.Rd spliceSites/man/readExpSet.Rd spliceSites/man/readMergedBamGaps.Rd spliceSites/man/readTabledBamGaps.Rd spliceSites/man/seqlogo.Rd spliceSites/man/silic_tryp.Rd spliceSites/man/sortTable-methods.Rd spliceSites/man/spliceSites-package.Rd spliceSites/man/trim.Rd spliceSites/man/truncateSeq.Rd spliceSites/man/truncate_seq.Rd spliceSites/man/trypsinCleave.Rd spliceSites/man/uniqueJuncAnn.Rd spliceSites/man/write.files.Rd spliceSites/man/xCodons.Rd spliceSites/man/xJunc.Rd spliceSites/man/xJuncStrand.Rd spliceSites/man/z[-methods.Rd
spliceSites/src
spliceSites/src/Makevars
spliceSites/src/Makevars.win
spliceSites/src/alpha_idx.h
spliceSites/src/spliceSites.c
spliceSites/src/spliceSites.h
spliceSites/vignettes
spliceSites/vignettes/spliceSites.Rnw
spliceSites/vignettes/spliceSites.bib

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