A B C D E G H I K L M N O P R S T U W misc
spliceSites-package | Calculate information on splice-sites from gapped alignments in RNA-seq data. |
aaGapSites-class | Class '"aaGapSites"' |
addGeneAlignPart | Reads a bamRange object for a given 'bamReader', 'refGenome' and gene name. |
addGeneAlignPart-method | Reads a bamRange object for a given 'bamReader', 'refGenome' and gene name. |
addHbond | Class '"hbond"' |
addHbond-method | Class '"hbond"' |
addHbond-methods | Class '"hbond"' |
addKeyTable | Class '"keyProfiler"' |
addKeyTable-method | Class '"keyProfiler"' |
addKeyTable-methods | Class '"keyProfiler"' |
addMaxEnt | addMaxEnt: Extract subset of data contained in given range given object. |
addMaxEnt-method | addMaxEnt: Extract subset of data contained in given range given object. |
addMaxEnt-methods | addMaxEnt: Extract subset of data contained in given range given object. |
alignGapList | Read 'gapSites' |
alt_left_ranks | alt_X_ranks functions |
alt_left_ranks-method | alt_X_ranks functions |
alt_left_ranks-methods | alt_X_ranks functions |
alt_ranks | alt_X_ranks functions |
alt_ranks-method | alt_X_ranks functions |
alt_ranks-methods | alt_X_ranks functions |
alt_right_ranks | alt_X_ranks functions |
alt_right_ranks-method | alt_X_ranks functions |
annGapSites-class | Class '"annGapSites"' |
annotate | Annotation functions for 'gapSites' objects |
annotate-method | Adds annotation data to existing ExpressionSet (created by 'readExpSet') |
annotate-method | Annotation functions for 'gapSites' objects |
annotate-methods | Annotation functions for 'gapSites' objects |
annotation | Annotation functions for 'gapSites' objects |
annotation-method | Annotation functions for 'gapSites' objects |
annotation-methods | Annotation functions for 'gapSites' objects |
annotation<- | Annotation functions for 'gapSites' objects |
annotation<--method | Annotation functions for 'gapSites' objects |
annotation<--methods | Annotation functions for 'gapSites' objects |
appendKeyTable | Class '"keyProfiler"' |
appendKeyTable-method | Class '"keyProfiler"' |
appendKeyTable-methods | Class '"keyProfiler"' |
as.data.frame-methods | 'as.data.frame' Returning content of data.frame. |
as.data.frame.cRanges | Class '"cRanges"': Centered ranges. |
as.data.frame.gapSites | Class '"gapSites"' |
basedir-method | Class '"hbond"' |
basedir-method | Class '"maxEnt"' |
basedir<--method | Class '"hbond"' |
basedir<--method | Class '"maxEnt"' |
c-method | Class '"cRanges"': Centered ranges. |
c-method | Class '"caRanges"' |
c-method | Class '"cdRanges"' |
c-method | Class '"gapSites"' |
c-methods | Coercing functions 'c'. |
caRanges-class | Class '"caRanges"' |
cdRanges-class | Class '"cdRanges"' |
count | Class '"cRanges"': Centered ranges. |
count-method | Class '"cRanges"': Centered ranges. |
count-methods | Class '"cRanges"': Centered ranges. |
countByGeneName | Reads align number for selected gene from multiple BAM-files. |
cRanges-class | Class '"cRanges"': Centered ranges. |
dim-method | Class '"cRanges"': Centered ranges. |
dim-method | Class '"gapSites"' |
dim-methods | 'dim': Return dimensions of contained data.frame. |
dnaGapSites | Creating 'gapSites' and 'dnaGapSites' objects. |
dnaGapSites-class | Class '"dnaGapSites"' |
dnaGapSites-method | Creating 'gapSites' and 'dnaGapSites' objects. |
dnaGapSites-methods | Creating 'gapSites' and 'dnaGapSites' objects. |
dnaRanges | Reads a bamRange object for a given 'bamReader', 'refGenome' and gene name. |
dnaRanges-method | Reads a bamRange object for a given 'bamReader', 'refGenome' and gene name. |
dnaRanges-methods | Reads a bamRange object for a given 'bamReader', 'refGenome' and gene name. |
do_group_align_data | Class '"gapSites"' |
end-method | Class '"cRanges"': Centered ranges. |
extractByGeneName | extractByGeneName: Extract subset for sites which lie in range(s) defined by given gene list. |
extractByGeneName-method | extractByGeneName: Extract subset for sites which lie in range(s) defined by given gene list. |
extractByGeneName-methods | extractByGeneName: Extract subset for sites which lie in range(s) defined by given gene list. |
extractRange | extractRange: Extract subset from object where records lie in given range. |
extractRange-method | extractRange: Extract subset from object where records lie in given range. |
extractRange-methods | extractRange: Extract subset from object where records lie in given range. |
gapSites | Creating 'gapSites' and 'dnaGapSites' objects. |
gapSites-class | Class '"gapSites"' |
getAnnStrand | Class '"gapSites"' |
getAnnStrand-method | Class '"gapSites"' |
getAnnStrand-methods | Class '"gapSites"' |
getGapSites | Read 'gapSites' |
getKeyTable | Class '"keyProfiler"' |
getKeyTable-method | Class '"keyProfiler"' |
getKeyTable-methods | Class '"keyProfiler"' |
getMeStrand | addMaxEnt: Extract subset of data contained in given range given object. |
getMeStrand-method | addMaxEnt: Extract subset of data contained in given range given object. |
getMeStrand-methods | addMaxEnt: Extract subset of data contained in given range given object. |
getProfile | Class '"gapSites"' |
getProfile-method | Class '"gapSites"' |
getProfile-methods | Class '"gapSites"' |
getSequence | Class '"cdRanges"' |
getSequence-method | Class '"caRanges"' |
getSequence-method | Class '"cdRanges"' |
getSequence-methods | Class '"cdRanges"' |
gptm | Class '"gapSites"' |
gptm-method | Class '"gapSites"' |
gptm-methods | Class '"gapSites"' |
hbond | Class '"hbond"' |
hbond-class | Class '"hbond"' |
hbond-method | Class '"hbond"' |
hbond-methods | Class '"hbond"' |
head-method | Class '"aaGapSites"' |
head-method | Class '"cRanges"': Centered ranges. |
head-method | Class '"caRanges"' |
head-method | Class '"cdRanges"' |
head-method | Class '"dnaGapSites"' |
head-method | Class '"gapSites"' |
head-methods | 'head' Return first lines of contained data.frame. |
id | Class '"cRanges"': Centered ranges. |
id-method | Class '"cRanges"': Centered ranges. |
id-methods | Class '"cRanges"': Centered ranges. |
initialize-method | Class '"SpliceCountSet"' |
initialize-method | Class '"cRanges"': Centered ranges. |
initialize-method | Class '"cdRanges"' |
initialize-method | Class '"keyProfiler"' |
initialize-methods | 'initialize' Initializing objects. |
keyProfiler-class | Class '"keyProfiler"' |
lCodons | xCodon methods |
lCodons-method | xCodon methods |
lCodons-methods | xCodon methods |
lend | Class '"gapSites"' |
lend-method | Class '"gapSites"' |
lend-methods | Class '"gapSites"' |
lJunc | xJunc methods: lJunc, rJunc, lrJunc |
lJunc-method | xJunc methods: lJunc, rJunc, lrJunc |
lJunc-methods | xJunc methods: lJunc, rJunc, lrJunc |
lJuncStrand | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand |
lJuncStrand-method | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand |
lJuncStrand-methods | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand |
load.hbond | Class '"hbond"' |
load.maxEnt | Class '"maxEnt"' |
lrCodons | lrCodon methods |
lrCodons-method | lrCodon methods |
lrCodons-methods | lrCodon methods |
lrJunc | xJunc methods: lJunc, rJunc, lrJunc |
lrJunc-method | xJunc methods: lJunc, rJunc, lrJunc |
lrJunc-methods | xJunc methods: lJunc, rJunc, lrJunc |
lrJuncStrand | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand |
lrJuncStrand-method | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand |
lrJuncStrand-methods | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand |
lstart | Class '"gapSites"' |
lstart-method | Class '"gapSites"' |
lstart-methods | Class '"gapSites"' |
maxEnt-class | Class '"maxEnt"' |
merge-methods | 'merge' Merging two objects into one. |
merge.gapSites | Class '"gapSites"' |
nAlignGaps | Class '"gapSites"' |
nAlignGaps-method | Class '"gapSites"' |
nAlignGaps-methods | Class '"gapSites"' |
nAligns | Class '"gapSites"' |
nAligns-method | Class '"gapSites"' |
nAligns-methods | Class '"gapSites"' |
overlap_genome | Class '"gapSites"' |
plot_diff | Class '"annGapSites"' |
plot_diff-method | Class '"annGapSites"' |
plot_diff-methods | Class '"annGapSites"' |
plot_diff_ranks | alt_X_ranks functions |
plot_diff_ranks-method | alt_X_ranks functions |
plot_diff_ranks-methods | alt_X_ranks functions |
rangeByGeneName | Reads a bamRange object for a given 'bamReader', 'refGenome' and gene name. |
rCodons | xCodon methods |
rCodons-method | xCodon methods |
rCodons-methods | xCodon methods |
readCuffGeneFpkm | Reads FPKM values into ExpressionSet. |
readExpSet | Reads gptm or rpmg value from all given BAM-files and all identified align gaps into ExpressionSet. |
readMergedBamGaps | Reads an object of type 'gapSites' using a vector of BAM file names. |
readTabledBamGaps | readTabledBamGaps function |
rend | Class '"gapSites"' |
rend-method | Class '"gapSites"' |
rend-methods | Class '"gapSites"' |
resize_left | trim and resize methods: trim_left, trim_right, resize_left, resize_right |
resize_left-method | trim and resize methods: trim_left, trim_right, resize_left, resize_right |
resize_left-methods | trim and resize methods: trim_left, trim_right, resize_left, resize_right |
resize_right | trim and resize methods: trim_left, trim_right, resize_left, resize_right |
resize_right-method | trim and resize methods: trim_left, trim_right, resize_left, resize_right |
resize_right-methods | trim and resize methods: trim_left, trim_right, resize_left, resize_right |
rJunc | xJunc methods: lJunc, rJunc, lrJunc |
rJunc-method | xJunc methods: lJunc, rJunc, lrJunc |
rJunc-methods | xJunc methods: lJunc, rJunc, lrJunc |
rJuncStrand | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand |
rJuncStrand-method | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand |
rJuncStrand-methods | xJuncStrand methods: lJuncStrand, rJuncStrand, lrJuncStrand |
rpmg | Class '"gapSites"' |
rpmg-method | Class '"gapSites"' |
rpmg-methods | Class '"gapSites"' |
rstart | Class '"gapSites"' |
rstart-method | Class '"gapSites"' |
rstart-methods | Class '"gapSites"' |
saveMaxEnt | Class '"maxEnt"' |
saveMaxEnt-method | Class '"maxEnt"' |
saveMaxEnt-methods | Class '"maxEnt"' |
score3 | Class '"maxEnt"' |
score3-method | Class '"maxEnt"' |
score3-methods | Class '"maxEnt"' |
score5 | Class '"maxEnt"' |
score5-method | Class '"maxEnt"' |
score5-methods | Class '"maxEnt"' |
scoreSeq3 | Class '"maxEnt"' |
scoreSeq3-method | Class '"maxEnt"' |
scoreSeq3-methods | Class '"maxEnt"' |
scoreSeq5 | Class '"maxEnt"' |
scoreSeq5-method | Class '"maxEnt"' |
scoreSeq5-methods | Class '"maxEnt"' |
seqid | Class '"gapSites"' |
seqid-method | Class '"cRanges"': Centered ranges. |
seqid-method | Class '"gapSites"' |
seqid-methods | Class '"gapSites"' |
seqlogo | Class '"cdRanges"' |
seqlogo-method | Class '"cdRanges"' |
seqlogo-method | Class '"dnaGapSites"' |
seqlogo-methods | Class '"cdRanges"' |
setMeStrand | addMaxEnt: Extract subset of data contained in given range given object. |
setMeStrand-method | addMaxEnt: Extract subset of data contained in given range given object. |
setMeStrand-methods | addMaxEnt: Extract subset of data contained in given range given object. |
show-method | Class '"aaGapSites"' |
show-method | Class '"cRanges"': Centered ranges. |
show-method | Class '"dnaGapSites"' |
show-method | Class '"gapSites"' |
silic_tryp | silic_tryp function |
sortTable | Class '"cRanges"': Centered ranges. |
sortTable-method | Class '"cRanges"': Centered ranges. |
sortTable-method | Class '"gapSites"' |
sortTable-methods | Sorting contained data with 'sortTable'. |
SpliceCountSet-class | Class '"SpliceCountSet"' |
spliceSites | Calculate information on splice-sites from gapped alignments in RNA-seq data. |
start-method | Class '"cRanges"': Centered ranges. |
strand | Class '"cRanges"': Centered ranges. |
strand-method | Class '"cRanges"': Centered ranges. |
strand-method | Class '"gapSites"' |
strand-methods | Class '"cRanges"': Centered ranges. |
strand<--method | Class '"gapSites"' |
translate | Class '"cdRanges"' |
translate-method | Class '"cdRanges"' |
translate-method | Class '"dnaGapSites"' |
translate-methods | Class '"cdRanges"' |
trim_left | trim and resize methods: trim_left, trim_right, resize_left, resize_right |
trim_left-method | trim and resize methods: trim_left, trim_right, resize_left, resize_right |
trim_left-methods | trim and resize methods: trim_left, trim_right, resize_left, resize_right |
trim_right | trim and resize methods: trim_left, trim_right, resize_left, resize_right |
trim_right-method | trim and resize methods: trim_left, trim_right, resize_left, resize_right |
trim_right-methods | trim and resize methods: trim_left, trim_right, resize_left, resize_right |
truncateSeq | truncateSeq method |
truncateSeq-method | truncateSeq method |
truncateSeq-methods | truncateSeq method |
truncate_seq | truncate_seq function |
trypsinCleave | trypsinCleave method |
trypsinCleave-method | trypsinCleave method |
trypsinCleave-methods | trypsinCleave method |
uniqueJuncAnn | uniqueJuncAnn method for ExpressionSet |
uniqueJuncAnn-method | uniqueJuncAnn method for ExpressionSet |
uniqueJuncAnn-methods | uniqueJuncAnn method for ExpressionSet |
width-method | Class '"cRanges"': Centered ranges. |
write.annDNA.tables | Class '"gapSites"' |
write.annDNA.tables-method | Class '"gapSites"' |
write.annDNA.tables-methods | Class '"gapSites"' |
write.files | write.files |
write.files-method | Class '"aaGapSites"' |
write.files-method | Class '"caRanges"' |
write.files-methods | write.files |
[-methods | Methods for Function '['. |