A B C F G L M N O P Q R S T U W misc
addAncestorGO | Add ancestor GO IDs |
axisTrack | Example data for plotting annotation. |
Axt | Class '"Axt"' |
Axt-class | Class '"Axt"' |
axtChain | axtChain |
axtInfo | axtInfo function |
binFromCoordRange | UCSC bin indexing system utility functions |
binRangesFromCoordRange | UCSC bin indexing system utility functions |
binRestrictionString | UCSC bin indexing system utility functions |
blatCNE | Wrapper function of blat for 'CNE' object |
c-method | Class '"Axt"' |
c-method | GRangePairs objects |
ceScan | ceScan function |
ceScan-method | ceScan function |
chainMergeSort | chainMergeSort |
chainNetSyntenic | chainNetSyntenic |
chainPreNet | chainPreNet |
class:GRangePairs | GRangePairs objects |
CNE | Class '"CNE"' |
CNE-class | Class '"CNE"' |
CNE12 | Class '"CNE"' |
CNE12-method | Class '"CNE"' |
CNE21 | Class '"CNE"' |
CNE21-method | Class '"CNE"' |
CNEDanRer10Hg38 | CNEHg38DanRer10 and CNEDanRer10Hg38 dataset |
CNEDensity | CNEDensity function |
CNEDensity-method | CNEDensity function |
CNEDensity-methods | CNEDensity function |
CNEFinal | Class '"CNE"' |
CNEFinal-method | Class '"CNE"' |
cneFinalListDanRer10Hg38 | cneFinalListDanRer10Hg38 dataset |
CNEHg38DanRer10 | CNEHg38DanRer10 and CNEDanRer10Hg38 dataset |
cneMerge | CNE merge function |
cneMerge-method | CNE merge function |
CNEMerged | Class '"CNE"' |
CNEMerged-method | Class '"CNE"' |
coerce-method | GRangePairs objects |
cpgIslands | Example data for plotting annotation. |
fetchChromSizes | fetchChromSizes function. |
first-method | GRangePairs objects |
fixCoordinates | Fix the coordinates in 'Axt' object |
fixCoordinates-method | Fix the coordinates in 'Axt' object |
GRangePairs | GRangePairs objects |
GRangePairs-class | GRangePairs objects |
grangesPairsForDotplot | grangesPairsForDotplot |
grglist-method | GRangePairs objects |
last | GRangePairs objects |
last-method | GRangePairs objects |
lastal | lastal wrapper |
lastz | lastz wrapper |
lavToPsl | lavToPsl |
length-method | Class '"Axt"' |
makeAncoraFiles | makeAncoraFiles |
makeAxtTracks | makeAxtTracks |
makeCNEDensity | Make 'Bed', 'bedGraph' and 'BigWig' files |
makeGRBs | makeGRBs |
matchDistribution | Plot the distribution of matched alignments. |
matchDistribution-method | Plot the distribution of matched alignments. |
N50 | Assembly statistics. |
N90 | Assembly statistics. |
netToAxt | netToAxt |
orgKEGGIds2EntrezIDs | Fetch mapping from KEGG IDs to Entrez IDs |
plotCNEDistribution | Plot sequential CNE number against CNE genomic location |
plotCNEWidth | Plot the CNE widths distribution |
psubAxt | Parallel subset of Axt alignment |
queryCNEData | Query the CNEData package to fetch the CNEs |
queryRanges | Class '"Axt"' |
queryRanges-method | Class '"Axt"' |
querySeqs | Class '"Axt"' |
querySeqs-method | Class '"Axt"' |
read.rmMask.GRanges | Read a RepeatMasker .out file |
read.rmskFasta | Read a soft repeat masked fasta |
readAncora | Read the cne file from Ancora format. |
readAncoraIntoSQLite | Read Ancora legacy CNE format |
readAxt | Read 'Axt' file |
readBed | Read bed file |
readCNERangesFromSQLite | readCNERangesFromSQLite function |
refGenes | Example data for plotting annotation. |
reverseCigar | reverseCigar function |
saveCNEToSQLite | Save CNE to SQLite |
score-method | Class '"Axt"' |
scoringMatrix | scoringMatrix |
second-method | GRangePairs objects |
seqinfo-method | GRangePairs objects |
seqnames-method | GRangePairs objects |
strand-method | GRangePairs objects |
subAxt | Subset an 'Axt' object |
subAxt-method | Subset an 'Axt' object |
subAxt-methods | Subset an 'Axt' object |
summary | Utility functions related to Axt alignment |
summary-method | Utility functions related to Axt alignment |
swap | GRangePairs objects |
swap-method | GRangePairs objects |
symCount | Class '"Axt"' |
symCount-method | Class '"Axt"' |
syntenicDotplot | Syntenic dotplot |
syntenicDotplot-method | Syntenic dotplot |
targetRanges | Class '"Axt"' |
targetRanges-method | Class '"Axt"' |
targetSeqs | Class '"Axt"' |
targetSeqs-method | Class '"Axt"' |
thresholds | Class '"CNE"' |
thresholds-method | Class '"CNE"' |
unique-method | GRangePairs objects |
unlist-method | GRangePairs objects |
writeAxt | 'writeAxt' function |
[-method | Class '"Axt"' |