Files in HTSeqGenie
A NGS analysis pipeline.
.BBSoptions
NEWS
NAMESPACE
DESCRIPTION
build/vignette.rds
R/picard.R
R/targetLengths.R
R/buildGenomicFeaturesFromTxDb.R
R/alignReads.R
R/config.R
R/bamUtils.R
R/coverage.R
R/trimReads.R
R/tools.R
R/analyzeVariants.R
R/TP53GenomicFeatures.R
R/io.R
R/detectRRNA.R
R/testHelpers.R
R/runPipeline.R
R/checkConfig.R
R/createSummaryCounts.R
R/initPipeline.R
R/wrapGsnap.R
R/mergeLanes.R
R/zzz.R
R/reportPipelineQA.R
R/gatk.R
R/detectAdapterContam.R
R/summaries.R
R/filterQuality.R
R/countGenomicFeatures.R
R/logging.R
R/preprocessReads.R
vignettes/RNASeq-pipeline-3.pdf
vignettes/HTSeqGenie.Rnw
vignettes/gene_models.jpeg
man/rpkm.Rd
man/tryKeepTraceback.Rd
man/removeChunkDir.Rd
man/getMemoryUsage.Rd
man/writeFastQFiles.Rd
man/hashVariants.Rd
man/listIterator.init.Rd
man/isConfig.Rd
man/writePreprocessAlignReport.Rd
man/buildConfig.Rd
man/saveWithID.Rd
man/safe.yield.Rd
man/getEndNumber.Rd
man/mergeAlignReads.Rd
man/writeVCF.Rd
man/mergePreprocessReads.Rd
man/gatk.Rd
man/writePreprocessAlignHTML.Rd
man/listIterator.next.Rd
man/preprocessReads.Rd
man/buildGenomicFeaturesFromTxDb.Rd
man/getConfig.logical.Rd
man/statCountFeatures.Rd
man/buildTP53GenomeTemplate.Rd
man/annotateVariants.Rd
man/TP53GenomicFeatures.Rd
man/callVariantsGATK.Rd
man/logdebug.Rd
man/writeFeatureCountsHTML.Rd
man/checkGATKJar.Rd
man/mergeLanes.Rd
man/logwarn.Rd
man/detectRRNA.Rd
man/getNumberOfReadsInFASTQFile.Rd
man/trimReads.Rd
man/hashCoverage.Rd
man/trimTailsByQuality.Rd
man/readInputFiles.Rd
man/initDirs.Rd
man/isAdapter.Rd
man/safeUnlink.Rd
man/getRRNAIds.Rd
man/mergeCoverage.Rd
man/truncateReads.Rd
man/plotDF.Rd
man/safeGetObject.Rd
man/getConfig.numeric.Rd
man/initPipelineFromSaveDir.Rd
man/readRNASeqEnds.Rd
man/isAboveQualityThresh.Rd
man/logerror.Rd
man/createTmpDir.Rd
man/checkPicardJar.Rd
man/resource.Rd
man/getConfig.integer.Rd
man/writeConfig.Rd
man/countFeatures.Rd
man/traceMem.Rd
man/runPipeline.Rd
man/detectQualityInFASTQFile.Rd
man/wrap.callVariants.Rd
man/analyzeVariants.Rd
man/HTSeqGenie.Rd
man/preprocessReadsChunk.Rd
man/FastQStreamer.init.Rd
man/calculateTargetLengths.Rd
man/initLogger.Rd
man/getBams.Rd
man/picard.Rd
man/FastQStreamer.release.Rd
man/buildTallyParam.Rd
man/filterByLength.Rd
man/excludeVariantsByRegions.Rd
man/mergeSummaryAlignment.Rd
man/countGenomicFeatures.Rd
man/realignIndelsGATK.Rd
man/isFirstFragment.Rd
man/calculateCoverage.Rd
man/updateConfig.Rd
man/getConfig.Rd
man/bamCountUniqueReads.Rd
man/isSparse.Rd
man/buildShortReadReports.Rd
man/setUpDirs.Rd
man/getChunkDirs.Rd
man/getPackageFile.Rd
man/makeDir.Rd
man/runPipelineConfig.Rd
man/processChunks.Rd
man/setChunkDir.Rd
man/buildTP53FastaGenome.Rd
man/findVariantFile.Rd
man/computeCoverage.Rd
man/initPipelineFromConfig.Rd
man/writeGenomicFeaturesReport.Rd
man/markDuplicates.Rd
man/alignReads.Rd
man/setupTestFramework.Rd
man/vcfStat.Rd
man/countGenomicFeaturesChunk.Rd
man/initLog.Rd
man/hashVector.Rd
man/loadConfig.Rd
man/markDups.Rd
man/relativeBarPlot.Rd
man/parseDCF.Rd
man/loginfo.Rd
man/getRandomAlignCutoff.Rd
man/getConfig.vector.Rd
man/getNumericVectorDataFromFile.Rd
man/makeRandomSreads.Rd
man/generateSingleGeneDERs.Rd
man/writeSummary.Rd
man/getTabDataFromFile.Rd
man/FastQStreamer.getReads.Rd
man/alignReadsChunk.Rd
man/filterQuality.Rd
man/computeBamStats.Rd
man/getObjectFilename.Rd
man/runAlignment.Rd
man/parseSummaries.Rd
man/checkConfig.Rd
man/realignIndels.Rd
man/getAdapterSeqs.Rd
man/runPreprocessReads.Rd
man/writeAudit.Rd
man/safeExecute.Rd
man/detectAdapterContam.Rd
man/sclapply.Rd
man/getTraceback.Rd
tests/doRUnit.R
inst/doc/HTSeqGenie.pdf
inst/doc/HTSeqGenie.Rnw
inst/doc/HTSeqGenie.R
inst/config/default-config.txt
inst/extdata/H1993_TP53_subset2500_1.fastq.gz
inst/extdata/H1993_TP53_subset2500_2.fastq.gz
inst/extdata/adapter_data/Illumina_adapters.curated.paired_end_2.fasta
inst/extdata/adapter_data/Illumina_adapters.curated.paired_end_1.fasta
inst/extdata/adapter_data/Illumina_adapters.curated.single_end.fasta
inst/extdata/adapter_data/Illumina_adapters.paired_end.fasta
inst/test-data/test_picard_dups.bam
inst/test-data/ndup-unmarked.bam
inst/test-data/SAM634406-subsample-config.txt
inst/test-data/tp53_rmsk.bed
inst/test-data/test_highqualSpliceInPE2SharedExonWithPE1.bam
inst/test-data/tp53_dbsnp.Rdata
inst/test-data/truncated.fastq.gz
inst/test-data/unit_tests_1.fastq
inst/test-data/unit_tests_2.fastq
inst/test-data/ndup-marked.bam
inst/test-data/test_config_single_end.txt
inst/test-data/SAM634406-subsample_R1.gz
inst/test-data/reads.fastq.gz
inst/test-data/braf_v600.vcf
inst/test-data/SAM634406-subsample_R2.gz
inst/test-data/test_config.txt
inst/test-data/empty.bam
inst/test-data/variant_calling/test_set.pair1.fastq
inst/test-data/variant_calling/test_set.merged.uniques.bam
inst/test-data/variant_calling/test_set.merged.uniques.bam.bai
inst/test-data/variant_calling/tp53_test.bam.bai
inst/test-data/variant_calling/tp53_test.bam
inst/test-data/variant_calling/one_variant_no_filtered.bam.bai
inst/test-data/variant_calling/test_set.pair2.fastq
inst/test-data/variant_calling/one_variant_no_filtered.bam
inst/test-data/bam_files_unit_test_PE/processed.aligner_input_2.fastq
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_mult.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_transloc.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_transloc.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_mult.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_mult.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_inv.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_inv.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_uniq.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_mult.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_uniq.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_uniq.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_transloc.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_mult.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_scr.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_scr.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_uniq.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_mult.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.nomapping.bam.bai
inst/test-data/bam_files_unit_test_PE/processed.aligner_input_1.fastq
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_long.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_transloc.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_mult.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_mult.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_transloc.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_uniq.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_long.bam
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_uniq.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_transloc.bam.bai
inst/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.nomapping.bam
inst/test-data/Realigner/KRAS_TP53_demo.dict
inst/test-data/Realigner/jiggling_indels_tp53_kras.bam
inst/test-data/Realigner/jiggling_indels.bam
inst/test-data/Realigner/jiggling_indels_tp53_kras.bam.bai
inst/test-data/Realigner/jiggling_indels.bam.bai
inst/unitTests/runit.config.R
inst/unitTests/runit.bamUtils.R
inst/unitTests/runit.runPipeline.R
inst/unitTests/runit.picard.R
inst/unitTests/runit.gatk.R
inst/unitTests/runit.tools.R
inst/unitTests/runit.calculateCoverage.R
inst/unitTests/runit.checkConfig.R
inst/unitTests/runit.preprocessReads.R
inst/unitTests/runit.filterQuality.R
inst/unitTests/runit.alignReads.R
inst/unitTests/runit.detectRRNA.R
inst/unitTests/runit.mergeLanes.R
inst/unitTests/runit.readRNASeqEnds.R
inst/unitTests/runTests.R
inst/unitTests/runit.analyzeVariants.R
inst/unitTests/runit.targetLengths.R
inst/unitTests/runit.buildGenomicFeatures.R
inst/unitTests/runit.reportPipelineQA.R
inst/unitTests/runit.trimReads.R
inst/unitTests/runit.io.R
inst/unitTests/runit.detectAdapterContam.R
