API for Bioconductor-mirror/customProDB
Generate customized protein database from NGS data, with a focus on RNA-Seq data, for proteomics search

Global functions
Bed2Range Man page Source code
Ensembl.fetchAttribTypeIdForTopLevelSequence Source code
Ensembl.fetchChromLengthsFromCoreUrl Source code
Ensembl.fetchTopLevelSequenceIds Source code
Ensembl.getFtpUrlToMySQL Source code
Ensembl.getMySQLCoreDir Source code
Ensembl.getMySQLCoreUrl Source code
Ensembl.getTable Source code
Ensembl.getTable.seq_region Source code
Ensembl.listMySQLCoreDirs Source code
InputVcf Man page Source code
JunctionType Man page Source code
Multiple_VCF Man page Source code
OutputNovelJun Man page Source code
OutputVarprocodingseq Man page Source code
OutputVarproseq Man page Source code
OutputVarproseq_single Man page Source code
Outputaberrant Man page Source code
Outputproseq Man page Source code
OutputsharedPro Man page Source code
Positionincoding Man page Source code
PrepareAnnotationEnsembl Man page Source code
PrepareAnnotationRefseq Man page Source code
SharedJunc Man page Source code
Varlocation Man page Source code
aaVariation Man page Source code
calculateRPKM Man page Source code
dbEasyPreparedQuery Source code
dbEasyQuery Source code
dbFileConnect Source code
debugSQL Source code
easyRun Man page Source code
easyRun_mul Man page Source code
extractCdsRangesFromBiomartTable Source code
extractEnsemblReleaseFromDbVersion Source code
extractSpeciesFromDatasetDesc Source code
fetchChromLengthsFromEnsembl Source code
gen_splicmatrix Source code Source code
getAllDatasetAttrGroups Source code
getBiomartDbVersion Source code
getChromInfoFromBiomart Source code
getDatasetAttrGroups Source code
getMartAttribList Source code
get_cached_dbconn Source code
get_cached_dbfile Source code
get_dbconn Source code
get_dbfile Source code
get_dbtable Source code
hasCol Source code
joinDataFrameWithName2Val Source code
lsFtpUrl Source code
makeBiomartChrominfo Source code
makeBiomartGenes Source code
makeBiomartSplicings Source code
makeBiomartTranscripts Source code
makeCdsDataFrameFromRanges Source code
makeExonRankCol Source code
makeIdsForUniqueDataFrameRows Source code
makeTranscriptDbFromBiomart_archive Source code
map2trans Source code
matchCircularity Source code
normUtrCoords Source code
parseBMFiltersParams Source code
parseBMMartParams Source code
parseBMValuesParams Source code
prepareBiomartMetadata Source code
scanMart Source code
scanMarts Source code
setDataFrameColClass Source code
Bioconductor-mirror/customProDB documentation built on June 1, 2017, 6:47 a.m.