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NAMESPACE
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NAMESPACE
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importFrom(data.table,"%between%", "%chin%", "%like%", ":=", as.data.table, between, chgroup, chmatch, chorder, CJ, copy, data.table, dcast, dcast.data.table, foverlaps,fread, haskey, key, "key<-", last, like,melt, set, setattr, setDF, setDT, setkey, setkeyv, setnames, setorder, setorderv)
importFrom("grDevices", "colorRampPalette", "dev.off", "pdf", "png",
"rainbow")
importFrom("graphics", "abline", "axTicks", "axis", "barplot", "box",
"clip", "hist", "lines", "mtext", "par", "pie", "plot",
"points", "rug", "text")
importFrom("stats", "density", "rt", "setNames")
importFrom("utils", "read.delim", "read.table", "write.table")
import(pheatmap)
import(RCurl)
import(Nozzle.R1)
import(stringr)
import(ggplot2)
import(S4Vectors)
import(IRanges)
import(GenomicRanges)
importFrom(Biostrings,DNAString,
AAStringSet, DNAStringSet, DNAStringSetList, DNA_BASES, getSeq ,
nchar, reverseComplement, substr, translate)
import(Rsamtools)
importFrom(GenomicFeatures,exonsBy,makeTxDbFromGFF,extractTranscriptSeqs)
import(RSQLite)
importFrom(rtracklayer,browserSession, ucscTableQuery,
tableNames, getTable, trackNames, ucscSchema,import,export)
importFrom(biomaRt, getBM, listAttributes, listDatasets, listMarts,
useDataset, useMart)
importFrom(GenomicFeatures, cdsBy, exons, transcripts,makeTxDbFromUCSC,
fiveUTRsByTranscript, threeUTRsByTranscript)
importFrom(VariantAnnotation, scanVcf, scanVcfHeader, samples)
importFrom(AnnotationDbi, loadDb, saveDb)
importFrom(customProDB,aaVariation,Bed2Range,InputVcf,JunctionType,
OutputNovelJun,Outputproseq,OutputVarproseq,
OutputVarproseq_single,Positionincoding,
PrepareAnnotationEnsembl,Varlocation)
importFrom(rTANDEM, rTParam, rTTaxo, setParamValue, tandem)
importFrom(dplyr, "%>%", filter, select, arrange, row_number,
distinct, group_by,rowwise,mutate,ungroup,bind_rows)
importFrom(processx,run)
importFrom(readr,write_tsv)
importFrom(seqinr,write.fasta)
export(dbCreator)
export(reportGear)
export(runTandem)
export(parserGear)
export(easyRun)
export(PrepareAnnotationEnsembl2)
export(PrepareAnnotationRefseq2)
export(createProDB4DenovoRNASeq)
export(addGeneName4Ensembl)
export(calculateFDR)
export(buildTargetDecoyDB)
export(buildFusionProteinDB)