Global functions | |
---|---|
..gmap | Source code |
..gsnap | Source code |
.atoiindex | Source code |
.bam_tally_C | Source code |
.cmetindex | Source code |
.commandLine | Source code |
.commandLine.handleMissingArgs | Source code |
.get_genome | Source code |
.gmap | Source code |
.gmapGenomeCreated | Source code |
.gmap_build | Source code |
.gsnap | Source code |
.iit_store | Source code |
.makeCdsIIT | Source code |
.make_iit_interval | Source code |
.normArgDb | Source code |
.snpindex | Source code |
.system | Source code |
.system_gsnap | Source code |
.test | Source code |
.valid_GmapOutput | Source code |
.valid_GsnapOutput | Source code |
.valid_GsnapParam | Source code |
.valid_GsnapParam_batch | Source code |
.valid_GsnapParam_format | Source code |
.valid_GsnapParam_max_mismatches | Source code |
.valid_GsnapParam_mode | Source code |
.valid_GsnapParam_nofails | Source code |
.valid_GsnapParam_novelsplicing | Source code |
.valid_GsnapParam_npaths | Source code |
.valid_GsnapParam_nthreads | Source code |
.valid_GsnapParam_part | Source code |
.valid_GsnapParam_quiet_if_excessive | Source code |
.valid_GsnapParam_read_group_id | Source code |
.valid_GsnapParam_read_group_name | Source code |
.valid_GsnapParam_splicing | Source code |
.valid_GsnapParam_split_output | Source code |
.valid_GsnapParam_suboptimal_levels | Source code |
.valid_GsnapParam_use_snps | Source code |
.valid_gmap_parameter | Source code |
BamTallyParam | Man page Source code |
BamTallyParam-class | Man page |
GeneGenome | Source code |
GmapAlignerParam_asList | Source code |
GmapBamReader | Source code |
GmapGenome | Man page Source code |
GmapGenome-class | Man page |
GmapGenomeDirectory | Man page Source code |
GmapGenomeDirectory-class | Man page |
GmapOutput | Source code |
GmapOutputList | Source code |
GmapParam | Source code |
GmapSnpDirectory | Man page Source code |
GmapSnpDirectory-class | Man page |
GmapSnps | Man page Source code |
GmapSnps-class | Man page |
GsnapOutput | Man page Source code |
GsnapOutput-class | Man page |
GsnapOutputList | Source code |
GsnapParam | Man page Source code |
GsnapParam-class | Man page |
IIT | Source code |
IITFile | Source code |
TP53Genome | Man page Source code |
TP53Which | Man page Source code |
TallyIIT | Source code |
[[<-,GmapSnpDirectory,ANY,ANY-method | Man page |
`gsnap_batch<-` | Source code |
`gsnap_extra<-` | Source code |
`gsnap_max_mismatches<-` | Source code |
`gsnap_mode<-` | Source code |
`gsnap_nofails<-` | Source code |
`gsnap_novelsplicing<-` | Source code |
`gsnap_npaths<-` | Source code |
`gsnap_nthreads<-` | Source code |
`gsnap_part<-` | Source code |
`gsnap_quiet_if_excessive<-` | Source code |
`gsnap_snpsdir<-` | Source code |
`gsnap_splicing<-` | Source code |
`gsnap_split_output<-` | Source code |
`gsnap_suboptimal_levels<-` | Source code |
`gsnap_use_snps<-` | Source code |
`iit<-` | Source code |
as.list,BamTallyParam-method | Man page |
as.list.GmapAlignerParam | Source code |
asSystemCall | Source code |
atoiindex | Source code |
bamFile | Source code |
bamPaths,GsnapOutput-method | Man page |
bam_tally | Man page |
bam_tally,BamFile-method | Man page |
bam_tally,GmapBamReader-method | Man page |
bam_tally,character-method | Man page |
bam_tally-methods | Man page |
checkPackageInstalled | Source code |
checkPackageVersion | Source code |
checkTallyConsistency | Source code |
close.IITFile | Source code |
cmetindex | Man page Source code |
coerce,BamTallyParam,list-method | Man page |
coerce,GmapGenome,DNAStringSet-method | Man page |
commandLine | Source code |
directory | Man page Source code |
directory,GmapSnps-method | Man page |
exonsOnTP53Genome | Source code |
fieldNames | Source code |
file_ext2 | Source code |
file_path_is_absolute | Source code |
file_path_is_dir | Source code |
formatToExt | Source code |
geneGenomeName | Source code |
geneOnTP53Genome | Source code |
genome,GmapGenome-method | Man page |
genome,GmapGenomeDirectory-method | Man page |
genome,TallyIIT-method | Man page |
getDefaultGmapGenomePath | Source code |
getDefaultGmapPath | Source code |
getExons | Source code |
getGeneRoi | Source code |
getSeq,GmapGenome-method | Man page |
gmapRange | Source code |
gmapVersion | Source code |
gmap_build,ANY,GmapGenome-method | Man page |
gmap_build,DNAStringSet,GmapGenome-method | Man page |
gmap_build,character,GmapGenome-method | Man page |
gmap_build-methods | Man page |
gsnap | Man page |
gsnap,character,character_OR_NULL,GsnapParam-method | Man page |
gsnap-methods | Man page |
gsnapInfo | Source code |
gsnapSucceeded | Source code |
gsnapVersion | Source code |
gsnap_batch | Source code |
gsnap_extra | Source code |
gsnap_max_mismatches | Source code |
gsnap_mode | Source code |
gsnap_nofails | Source code |
gsnap_novelsplicing | Source code |
gsnap_npaths | Source code |
gsnap_nthreads | Source code |
gsnap_part | Source code |
gsnap_quiet_if_excessive | Source code |
gsnap_snpsdir | Source code |
gsnap_splicing | Source code |
gsnap_split_output | Source code |
gsnap_suboptimal_levels | Source code |
gsnap_use_snps | Source code |
guessReadLengthFromBam | Source code |
iit | Source code |
is_dir | Source code |
length,GmapSnpDirectory-method | Man page |
makeGmapGenomePackage | Man page Source code |
mapsDirectory | Source code |
names,GmapSnpDirectory-method | Man page |
newGmapAlignerOutput | Source code |
newGmapAlignerParam | Source code |
normArgFields | Source code |
normArgSingleCharacterOrNULL | Source code |
normArgSingleInteger | Source code |
normArgSingleNumber | Source code |
normArgTRUEorFALSE | Source code |
normArgType | Source code |
normArgWhich | Source code Source code |
normalizeIndelAlleles | Source code |
open.IITFile | Source code |
openForWhich | Source code |
parseGsnapVersion | Source code |
path,GmapBamReader-method | Man page |
path,GmapGenome-method | Man page |
path,GmapGenomeDirectory-method | Man page |
path,GmapSnpDirectory-method | Man page |
path,GsnapOutput-method | Man page |
path,NULL-method | Man page |
paths | Source code |
samPaths | Source code |
seqinfo,GmapGenome-method | Man page |
showSlot | Source code |
showSlots | Source code |
snpindex | Source code |
snps<- | Man page |
snps<-,GmapGenome,ANY,ANY-method | Man page |
snps<-,GmapSnpDirectory,character,VCF-method | Man page |
snps<-,GmapSnpDirectory,character,character-method | Man page |
spliceSites<- | Man page |
spliceSites<-,GmapGenome,GRangesList-method | Man page |
spliceSites<-,GmapGenome,TxDb-method | Man page |
subsetRegion | Source code |
translateToP53Genome | Source code |
typeNames | Source code |
variantSummary | Man page Source code |
variantSummaryColumnDescriptions | Source code |
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