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

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Search the wokai/spliceSites package
Functions
272
Source code
7
Man pages
50
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wokai/spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data
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API

API for wokai/spliceSites
A bioconductor package for exploration of alignment gap positions from RNA-seq data

Global functions
SpliceCountSet-class Man page
[,cRanges-method Man page
[,gapSites-method Man page
[-methods Man page
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,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
as.data.frame.gapSites Man page
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
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-method Man page
dnaRanges-methods Man page
do_group_align_data Man page
end,cRanges-method Man page
extractByGeneName Man page
extractByGeneName,cRanges-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
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,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
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-methods Man page
merge.gapSites 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
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
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
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
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
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
truncateSeq Man page
truncateSeq,aaGapSites-method Man page
truncateSeq,caRanges-method Man page
truncateSeq-methods Man page
truncate_seq 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-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
wokai/spliceSites documentation built on May 4, 2019, 9:46 a.m.

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