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
Version1.22.1

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 '['.

Functions

aaGapSites-class Man page
addGeneAligns Man page
addGeneAligns,gapSites-method Man page
addGeneAligns-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
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<- Man page
annotation<-,gapSites,ANY-method Man page
annotation,gapSites-method Man page
annotation<-,gapSites,refJunctions-method Man page
annotation<--methods Man page
annotation-methods Man page
appendKeyTable Man page
appendKeyTable,keyProfiler-method Man page
appendKeyTable-methods Man page
as.data.frame.cRanges Man page
as.data.frame.gapSites Man page
as.data.frame-methods Man page
basedir<-,hbond-method Man page
basedir,hbond-method Man page
basedir<-,maxEnt-method Man page
basedir,maxEnt-method Man page
caRanges-class Man page
c,caRanges-method Man page
c,cdRanges-method Man page
c,cRanges-method Man page
cdRanges-class Man page
c,gapSites-method Man page
c-methods Man page
count Man page
countByGeneName Man page
count,cRanges-method Man page
count-methods Man page
cRanges-class Man page
[,cRanges-method Man page
dim,cRanges-method Man page
dim,gapSites-method Man page
dim-methods Man page
dnaGapSites Man page
dnaGapSites-class Man page
dnaGapSites,gapSites,DNAStringSet-method 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
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
gapSites-class Man page
[,gapSites-method Man page
getAnnStrand Man page
getAnnStrand,gapSites-method Man page
getAnnStrand-methods Man page
getGapSites Man page
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
gptm Man page
gptm,gapSites-method Man page
gptm-methods Man page
hbond Man page
hbond-class Man page
hbond,hbond-method Man page
hbond-methods Man page
head,aaGapSites-method Man page
head,caRanges-method Man page
head,cdRanges-method Man page
head,cRanges-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,cdRanges-method Man page
initialize,cRanges-method Man page
initialize,keyProfiler-method Man page
initialize-methods Man page
initialize,SpliceCountSet-method Man page
keyProfiler-class Man page
lCodons Man page
lCodons,cRanges-method Man page
lCodons-methods Man page
lend Man page
lend,gapSites-method Man page
lend-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
load.hbond Man page
load.maxEnt Man page
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.gapSites Man page
merge-methods Man page
[-methods Man page
nAlignGaps Man page
nAlignGaps,gapSites-method Man page
nAlignGaps-methods Man page
nAligns Man page
nAligns,gapSites-method Man page
nAligns-methods Man page
overlap_genome 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
plotGeneAlignDepth Man page
plotGeneAlignDepth,bamReader-method Man page
plotGeneAlignDepth-methods Man page
rangeByGeneName Man page
rCodons Man page
rCodons,cRanges-method Man page
rCodons-methods Man page
readCuffGeneFpkm Man page
readExpSet Man page
readMergedBamGaps Man page
readTabledBamGaps Man page
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
rJunc Man page
rJunc,gapSites-method Man page
rJunc-methods Man page
rJuncStrand Man page
rJuncStrand,gapSites-method Man page
rJuncStrand-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
seqid,gapSites-method 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
sortTable Man page
sortTable,cRanges-method Man page
sortTable,gapSites-method Man page
sortTable-methods Man page
SpliceCountSet-class 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,gapSites-method Man page
strand-methods Man page
translate Man page
translate,cdRanges-method Man page
translate,dnaGapSites-method Man page
translate-methods Man page
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
truncate_seq Man page
truncateSeq Man page
truncateSeq,aaGapSites-method Man page
truncateSeq,caRanges-method Man page
truncateSeq-methods Man page
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

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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