Man pages for omicsCore/SEQprocess
SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.
| bowtie2 | bowtie2 |
| build.star.idx | STAR |
| bwa | bwa |
| cufflinks | cufflinks |
| cutadapt | cutadapt |
| eset2SE | eset2SE |
| fastQC | fastQC |
| gatk.baserecalibrator | gatk.baserecalibrator |
| gatk.combinevariants | gatk.combinevariants |
| gatk.depthOFcoverage | gatk.depthOFcoverage |
| gatk.haplotypecaller | gatk.haplotypecaller |
| gatk.mutect2.normal | gatk.mutect2.normal |
| gatk.printreads | gatk.printreads |
| gatk.realign | gatk.realign |
| gatk.targetcreator | gatk.targetcreator |
| gatk.variantfilter | gatk.variantfilter |
| generate.GC | generate.GC |
| get.annovar.report | get.annovar.report |
| get.collectmetrics.report | get.collectmetrics.report |
| get.fns | get.fns |
| get.process.names | get.process.names |
| get.proc.report | get.proc.report |
| get.qc.report | get.qc.report |
| get.Robject.report | get.Robject.report |
| get.single_end.metrics.report | get.single.end.metrics.report |
| get.tophat.report | get.tophat.report |
| get.trim_cut.report | get.trim_cut.report |
| get.trim.gal.report | get.trim.gal.report |
| gff2gr | gff2gr |
| gtf2gr | gtf2gr |
| htseq.add.info | htseq.add.info |
| htseq_count | htseq_count |
| make.cset | make.cset |
| make.eset | make.eset |
| make.vset | make.vset |
| multiple.reads.pileup | multiple.reads.pileup |
| MuSE.call | MuSE.call |
| MuSE.sump | MuSE.sump |
| Muse.tabix2.vcf | VCFtabix |
| mutect2 | mutect2 |
| mut.type.somatic | mut.type.somatic |
| picard.addrg | picard.addrg |
| picard.collectmetrics | picard.collectmetrics |
| picard.reorder | picard.reorder |
| picard.rmdu | picard.rmdu |
| pileup2seqz | generate.seqz |
| ploidyNcellularity | ploidyNcellularity |
| print_message | print_message |
| processSomatic | processSomatic |
| qc_aggregate | qc_aggregate |
| read.pileup.gz | read.pileup.gz |
| refGene2gr | refGene2gr |
| report | report |
| SEQprocess | SEQprocess |
| seqz2rda | seqz2rda |
| seqz2seg | seqz2seg |
| somaticsniper | somaticsniper |
| STAR | STAR |
| table.annovar | table.annovar |
| tophat2 | tophat2 |
| trim.gal | trim.gal |
| varscan | varscan |
| vcf2annovar | vcf2annovar |
| vcf2gz | vcf2gz |
| vep | Vairant Effect Predictor (VEP) |
| vset.preprocess | vset.preprocess |
