spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data
Version 1.24.0

Performs splice centered analysis on RNA-seq data.

AuthorWolfgang Kaisers
Bioconductor views DifferentialExpression GeneExpression Proteomics RNAseq
Date of publicationNone
MaintainerWolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
LicenseGPL-2
Version1.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("spliceSites")

Getting started

Package overview

Popular man pages

addGenomeData-ExpressionSet: Add MaxEnt-scores, Exon-Intron junction sequences score to...
caRanges-class: Class '"caRanges"'
cRanges-class: Class '"cRanges"': Centered ranges.
extractByGeneName: extractByGeneName: Extract subset for sites which lie in...
lrCodons: lrCodon methods
maxEnt-class: Class '"maxEnt"'
xCodons: xCodon methods
See all...

All man pages Function index File listing

Man pages

aaGapSites-class: Class '"aaGapSites"'
addGeneAligns: Reads a bamRange object for a given 'bamReader', 'refGenome'...
addGenomeData-ExpressionSet: Add MaxEnt-scores, Exon-Intron junction sequences score to...
addGenomeData-gapSites: Add MaxEnt-scores, Exon-Intron junction sequences score to...
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 '['.

Functions

SpliceCountSet-class Man page
[,cRanges-method Man page
[,gapSites,ANY,ANY,ANY-method Man page
[-methods Man page
aaGapSites-class Man page
addGeneAligns Man page
addGeneAligns,gapSites-method Man page
addGeneAligns-method Man page
addGenomeData Man page
addGenomeData,ExpressionSet,DNAStringSet,refJunctions-method Man page
addGenomeData,gapSites,DNAStringSet,refJunctions-method Man page
addGenomeData-method Man page
addHbond Man page
addHbond,cdRanges-method Man page
addHbond,gapSites-method Man page
addHbond-methods Man page
addKeyTable Man page
addKeyTable,keyProfiler-method Man page
addKeyTable-methods Man page
addMaxEnt Man page
addMaxEnt,gapSites-method Man page
addMaxEnt-methods Man page
alignGapList Man page Source code
alignGapProbes Source code
alphabetIndex Source code
alt_left_ranks Man page
alt_left_ranks,gapSites-method Man page
alt_left_ranks-methods Man page
alt_ranks Man page
alt_ranks,gapSites-method Man page
alt_ranks-methods Man page
alt_right_ranks Man page
alt_right_ranks,gapSites-method Man page
alt_right_ranks-method Man page
annGapSites-class Man page
annotate Man page
annotate,ExpressionSet,refJunctions-method Man page
annotate,gapSites,refJunctions-method Man page
annotate-methods Man page
annotation Man page
annotation,gapSites-method Man page
annotation-methods Man page
annotation<- Man page
annotation<-,gapSites,ANY-method Man page
annotation<-,gapSites,refJunctions-method Man page
annotation<--methods Man page
appendKeyTable Man page
appendKeyTable,keyProfiler-method Man page
appendKeyTable-methods Man page
as.data.frame-methods Man page
as.data.frame.cRanges Man page Source code
as.data.frame.gapSites Man page Source code
basedir,hbond-method Man page
basedir,maxEnt-method Man page
basedir<-,hbond-method Man page
basedir<-,maxEnt-method Man page
c,cRanges-method Man page
c,caRanges-method Man page
c,cdRanges-method Man page
c,gapSites-method Man page
c-methods Man page
cRanges-class Man page
caRanges-class Man page
cdRanges-class Man page
count Man page
count,cRanges-method Man page
count-methods Man page
countByGeneName Man page Source code
dim,cRanges-method Man page
dim,gapSites-method Man page
dim-methods Man page
dnaGapSites Man page
dnaGapSites,gapSites,DNAStringSet-method Man page
dnaGapSites-class Man page
dnaGapSites-methods Man page
dnaRanges Man page
dnaRanges,cRanges,DNAStringSet,logical-method Man page
dnaRanges,cRanges,DNAStringSet,missing-method Man page
dnaRanges,cRanges-method Man page
dnaRanges-methods Man page
do_group_align_data Man page Source code
end,cRanges-method Man page
extractByGeneName Man page
extractByGeneName,cRanges,ANY-method Man page
extractByGeneName,cRanges-method Man page
extractByGeneName,gapSites,ANY-method Man page
extractByGeneName,gapSites-method Man page
extractByGeneName-methods Man page
extractRange Man page
extractRange,cRanges-method Man page
extractRange,gapSites-method Man page
extractRange-methods Man page
gapSites Man page Source code
gapSites-class Man page
getAnnStrand Man page
getAnnStrand,gapSites-method Man page
getAnnStrand-methods Man page
getDataFrame Source code
getGapSites Man page Source code
getKeyTable Man page
getKeyTable,keyProfiler-method Man page
getKeyTable-methods Man page
getMeStrand Man page
getMeStrand,gapSites-method Man page
getMeStrand-methods Man page
getProfile Man page
getProfile,gapSites-method Man page
getProfile-methods Man page
getSequence Man page
getSequence,caRanges-method Man page
getSequence,cdRanges-method Man page
getSequence-methods Man page
get_dna_nmers Source code
gptm Man page
gptm,gapSites-method Man page
gptm-methods Man page
hbond Man page
hbond,hbond-method Man page
hbond-class Man page
hbond-methods Man page
head,aaGapSites-method Man page
head,cRanges-method Man page
head,caRanges-method Man page
head,cdRanges-method Man page
head,dnaGapSites-method Man page
head,gapSites-method Man page
head-methods Man page
id Man page
id,cRanges-method Man page
id-methods Man page
initialize,SpliceCountSet-method Man page
initialize,cRanges-method Man page
initialize,cdRanges-method Man page
initialize,keyProfiler-method Man page
initialize-methods Man page
keyProfiler-class Man page
lCodons Man page
lCodons,cRanges-method Man page
lCodons-methods Man page
lJunc Man page
lJunc,gapSites-method Man page
lJunc-methods Man page
lJuncStrand Man page
lJuncStrand,gapSites-method Man page
lJuncStrand-methods Man page
lend Man page
lend,gapSites-method Man page
lend-methods Man page
load.hbond Man page Source code
load.maxEnt Man page Source code
lrCodons Man page
lrCodons,gapSites-method Man page
lrCodons-methods Man page
lrJunc Man page
lrJunc,gapSites-method Man page
lrJunc-methods Man page
lrJuncStrand Man page
lrJuncStrand,gapSites-method Man page
lrJuncStrand-methods Man page
lstart Man page
lstart,gapSites-method Man page
lstart-methods Man page
maxEnt-class Man page
merge-methods Man page
merge.gapSites Man page Source code
nAlignGaps Man page
nAlignGaps,gapSites-method Man page
nAlignGaps-methods Man page
nAligns Man page
nAligns,gapSites-method Man page
nAligns-methods Man page
onUnload Source code Source code
overlap_genome Man page Source code
padd Source code
plotGeneAlignDepth Man page
plotGeneAlignDepth,bamReader-method Man page
plotGeneAlignDepth-methods Man page
plot_diff Man page
plot_diff,annGapSites-method Man page
plot_diff-methods Man page
plot_diff_ranks Man page
plot_diff_ranks,gapSites-method Man page
plot_diff_ranks-methods Man page
rCodons Man page
rCodons,cRanges-method Man page
rCodons-methods Man page
rJunc Man page
rJunc,gapSites-method Man page
rJunc-methods Man page
rJuncStrand Man page
rJuncStrand,gapSites-method Man page
rJuncStrand-methods Man page
rangeByGeneName Man page Source code
read.maxEnt Source code
readCuffGeneFpkm Man page Source code
readExpSet Man page Source code
readMergedBamGaps Man page Source code
readTabledBamGaps Man page Source code
rend Man page
rend,gapSites-method Man page
rend-methods Man page
resize_left Man page
resize_left,gapSites-method Man page
resize_left-methods Man page
resize_right Man page
resize_right,gapSites-method Man page
resize_right-methods Man page
rpmg Man page
rpmg,gapSites-method Man page
rpmg-methods Man page
rstart Man page
rstart,gapSites-method Man page
rstart-methods Man page
saveMaxEnt Man page
saveMaxEnt,maxEnt-method Man page
saveMaxEnt-methods Man page
score3 Man page
score3,maxEnt-method Man page
score3-methods Man page
score5 Man page
score5,maxEnt-method Man page
score5-methods Man page
scoreSeq3 Man page
scoreSeq3,maxEnt-method Man page
scoreSeq3-methods Man page
scoreSeq5 Man page
scoreSeq5,maxEnt-method Man page
scoreSeq5-methods Man page
seqid Man page
seqid,cRanges-method Man page
seqid,gapSites-method Man page Man page
seqid-methods Man page
seqlogo Man page
seqlogo,cdRanges-method Man page
seqlogo,dnaGapSites-method Man page
seqlogo-methods Man page
setMeStrand Man page
setMeStrand,gapSites-method Man page
setMeStrand-methods Man page
show,aaGapSites-method Man page
show,cRanges-method Man page
show,dnaGapSites-method Man page
show,gapSites-method Man page
silic_tryp Man page Source code
sortTable Man page
sortTable,cRanges-method Man page
sortTable,gapSites-method Man page
sortTable-methods Man page
spliceSites Man page
spliceSites-package Man page
start,cRanges-method Man page
strand Man page
strand,cRanges-method Man page
strand,gapSites-method Man page
strand-methods Man page
strand<-,gapSites-method Man page
translate Man page
translate,cdRanges-method Man page
translate,dnaGapSites-method Man page
translate-methods Man page
trclv Source code
trim_left Man page
trim_left,gapSites-method Man page
trim_left-methods Man page
trim_right Man page
trim_right,gapSites-method Man page
trim_right-methods Man page
trnctsq Source code
truncateSeq Man page
truncateSeq,aaGapSites-method Man page
truncateSeq,caRanges-method Man page
truncateSeq-methods Man page
truncate_seq Man page Source code
trypsinCleave Man page
trypsinCleave,aaGapSites-method Man page
trypsinCleave,caRanges-method Man page
trypsinCleave-methods Man page
uniqueJuncAnn Man page
uniqueJuncAnn,ExpressionSet,refJunctions-method Man page
uniqueJuncAnn-methods Man page
width,cRanges-method Man page
write.annDNA.tables Man page
write.annDNA.tables,gapSites,DNAStringSet,character-method Man page
write.annDNA.tables-methods Man page
write.files Man page
write.files,aaGapSites-method Man page
write.files,caRanges-method Man page
write.files-methods Man page

Files

ChangeLog
DESCRIPTION
NAMESPACE
NEWS
R
R/allClasses.R
R/allGenerics.R
R/c-methods.R
R/dim-methods.R
R/head-methods.R
R/show-methods.R
R/spliceSites.R
build
build/vignette.rds
inst
inst/doc
inst/doc/spliceSites.R
inst/doc/spliceSites.Rnw
inst/doc/spliceSites.pdf
inst/extdata
inst/extdata/cuff_files
inst/extdata/cuff_files/1.genes.fpkm_tracking
inst/extdata/cuff_files/10.genes.fpkm_tracking
inst/extdata/cuff_files/2.genes.fpkm_tracking
inst/extdata/cuff_files/3.genes.fpkm_tracking
inst/extdata/cuff_files/4.genes.fpkm_tracking
inst/extdata/cuff_files/5.genes.fpkm_tracking
inst/extdata/cuff_files/6.genes.fpkm_tracking
inst/extdata/cuff_files/7.genes.fpkm_tracking
inst/extdata/cuff_files/8.genes.fpkm_tracking
inst/extdata/cuff_files/9.genes.fpkm_tracking
inst/extdata/cuff_files/groups.csv
inst/extdata/dna_small.RData
inst/extdata/ens_small.RData
inst/extdata/hbs.RData
inst/extdata/key.RData
inst/extdata/maxent.RData
inst/extdata/rna_fem.bam
inst/extdata/rna_fem.bam.bai
inst/extdata/rna_mal.bam
inst/extdata/rna_mal.bam.bai
inst/extdata/uc_small.RData
inst/extdata/uc_small_junc.RData
man
man/SpliceCountSet-class.Rd
man/aaGapSites-class.Rd
man/addGeneAligns.Rd
man/addGenomeData-ExpressionSet.Rd
man/addGenomeData-gapSites.Rd
man/addHbond.Rd
man/addMaxEnt.Rd
man/alt_X_ranks.Rd
man/annGapSites-class.Rd
man/annotate-ExpressionSet.Rd
man/annotation.Rd
man/as.data.frame-methods.Rd
man/c-methods.Rd
man/cRanges-class.Rd
man/caRanges-class.Rd
man/cdRanges-class.Rd
man/countByGeneName.Rd
man/dim-methods.Rd
man/dnaGapSites-class.Rd
man/dnaRanges.Rd
man/extractByGeneName.Rd
man/extractRange.Rd
man/gapSites-class.Rd
man/gapSites.Rd
man/getGapSites.Rd
man/hbond-class.Rd
man/head-methods.Rd
man/initialize-methods.Rd
man/keyProfiler-class.Rd
man/lrCodons.Rd
man/maxEnt-class.Rd
man/merge-methods.Rd
man/plotGeneAlignDepth.Rd
man/rangeByGeneName.Rd
man/readCuffGeneFpkm.Rd
man/readExpSet.Rd
man/readMergedBamGaps.Rd
man/readTabledBamGaps.Rd
man/seqlogo.Rd
man/silic_tryp.Rd
man/sortTable-methods.Rd
man/spliceSites-package.Rd
man/trim.Rd
man/truncateSeq.Rd
man/truncate_seq.Rd
man/trypsinCleave.Rd
man/uniqueJuncAnn.Rd
man/write.files.Rd
man/xCodons.Rd
man/xJunc.Rd
man/xJuncStrand.Rd
man/z[-methods.Rd
src
src/Makevars
src/Makevars.win
src/alpha_idx.h
src/spliceSites.c
src/spliceSites.h
vignettes
vignettes/spliceSites.Rnw
vignettes/spliceSites.bib
spliceSites documentation built on May 20, 2017, 10:41 p.m.

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