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

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Performs splice centered analysis on RNA-seq data.

Author
Wolfgang Kaisers
Date of publication
None
Maintainer
Wolfgang Kaisers <kaisers@med.uni-duesseldorf.de>
License
GPL-2
Version
1.22.0

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