lib/R/library/HTSeqGenie/DESCRIPTION
lib/R/library/HTSeqGenie/INDEX
lib/R/library/HTSeqGenie/Meta/Rd.rds
lib/R/library/HTSeqGenie/Meta/features.rds
lib/R/library/HTSeqGenie/Meta/hsearch.rds
lib/R/library/HTSeqGenie/Meta/links.rds
lib/R/library/HTSeqGenie/Meta/nsInfo.rds
lib/R/library/HTSeqGenie/Meta/package.rds
lib/R/library/HTSeqGenie/Meta/vignette.rds
lib/R/library/HTSeqGenie/NAMESPACE
lib/R/library/HTSeqGenie/NEWS
lib/R/library/HTSeqGenie/R/HTSeqGenie
lib/R/library/HTSeqGenie/R/HTSeqGenie.rdb
lib/R/library/HTSeqGenie/R/HTSeqGenie.rdx
lib/R/library/HTSeqGenie/config/default-config.txt
lib/R/library/HTSeqGenie/doc/HTSeqGenie.R
lib/R/library/HTSeqGenie/doc/HTSeqGenie.Rnw
lib/R/library/HTSeqGenie/doc/HTSeqGenie.pdf
lib/R/library/HTSeqGenie/doc/index.html
lib/R/library/HTSeqGenie/extdata/H1993_TP53_subset2500_1.fastq.gz
lib/R/library/HTSeqGenie/extdata/H1993_TP53_subset2500_2.fastq.gz
lib/R/library/HTSeqGenie/extdata/adapter_data/Illumina_adapters.curated.paired_end_1.fasta
lib/R/library/HTSeqGenie/extdata/adapter_data/Illumina_adapters.curated.paired_end_2.fasta
lib/R/library/HTSeqGenie/extdata/adapter_data/Illumina_adapters.curated.single_end.fasta
lib/R/library/HTSeqGenie/extdata/adapter_data/Illumina_adapters.paired_end.fasta
lib/R/library/HTSeqGenie/help/AnIndex
lib/R/library/HTSeqGenie/help/HTSeqGenie.rdb
lib/R/library/HTSeqGenie/help/HTSeqGenie.rdx
lib/R/library/HTSeqGenie/help/aliases.rds
lib/R/library/HTSeqGenie/help/paths.rds
lib/R/library/HTSeqGenie/html/00Index.html
lib/R/library/HTSeqGenie/html/R.css
lib/R/library/HTSeqGenie/test-data/Realigner/KRAS_TP53_demo.dict
lib/R/library/HTSeqGenie/test-data/Realigner/jiggling_indels.bam
lib/R/library/HTSeqGenie/test-data/Realigner/jiggling_indels.bam.bai
lib/R/library/HTSeqGenie/test-data/Realigner/jiggling_indels_tp53_kras.bam
lib/R/library/HTSeqGenie/test-data/Realigner/jiggling_indels_tp53_kras.bam.bai
lib/R/library/HTSeqGenie/test-data/SAM634406-subsample-config.txt
lib/R/library/HTSeqGenie/test-data/SAM634406-subsample_R1.gz
lib/R/library/HTSeqGenie/test-data/SAM634406-subsample_R2.gz
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/processed.aligner_input_1.fastq
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/processed.aligner_input_2.fastq
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_mult.bam
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_mult.bam.bai
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_transloc.bam
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_transloc.bam.bai
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_uniq.bam
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.concordant_uniq.bam.bai
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_mult.bam
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_mult.bam.bai
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_transloc.bam
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_transloc.bam.bai
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_uniq.bam
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.halfmapping_uniq.bam.bai
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.nomapping.bam
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.nomapping.bam.bai
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_mult.bam
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_mult.bam.bai
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_inv.bam
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_inv.bam.bai
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_long.bam
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_long.bam.bai
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_scr.bam
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.paired_uniq_scr.bam.bai
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_mult.bam
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_mult.bam.bai
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_transloc.bam
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_transloc.bam.bai
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_uniq.bam
lib/R/library/HTSeqGenie/test-data/bam_files_unit_test_PE/test_pe.gsnap.merged.unpaired_uniq.bam.bai
lib/R/library/HTSeqGenie/test-data/braf_v600.vcf
lib/R/library/HTSeqGenie/test-data/empty.bam
lib/R/library/HTSeqGenie/test-data/ndup-marked.bam
lib/R/library/HTSeqGenie/test-data/ndup-unmarked.bam
lib/R/library/HTSeqGenie/test-data/reads.fastq.gz
lib/R/library/HTSeqGenie/test-data/test_config.txt
lib/R/library/HTSeqGenie/test-data/test_config_single_end.txt
lib/R/library/HTSeqGenie/test-data/test_highqualSpliceInPE2SharedExonWithPE1.bam
lib/R/library/HTSeqGenie/test-data/test_picard_dups.bam
lib/R/library/HTSeqGenie/test-data/tp53_dbsnp.Rdata
lib/R/library/HTSeqGenie/test-data/tp53_rmsk.bed
lib/R/library/HTSeqGenie/test-data/truncated.fastq.gz
lib/R/library/HTSeqGenie/test-data/unit_tests_1.fastq
lib/R/library/HTSeqGenie/test-data/unit_tests_2.fastq
lib/R/library/HTSeqGenie/test-data/variant_calling/one_variant_no_filtered.bam
lib/R/library/HTSeqGenie/test-data/variant_calling/one_variant_no_filtered.bam.bai
lib/R/library/HTSeqGenie/test-data/variant_calling/test_set.merged.uniques.bam
lib/R/library/HTSeqGenie/test-data/variant_calling/test_set.merged.uniques.bam.bai
lib/R/library/HTSeqGenie/test-data/variant_calling/test_set.pair1.fastq
lib/R/library/HTSeqGenie/test-data/variant_calling/test_set.pair2.fastq
lib/R/library/HTSeqGenie/test-data/variant_calling/tp53_test.bam
lib/R/library/HTSeqGenie/test-data/variant_calling/tp53_test.bam.bai
lib/R/library/HTSeqGenie/unitTests/runTests.R
lib/R/library/HTSeqGenie/unitTests/runit.alignReads.R
lib/R/library/HTSeqGenie/unitTests/runit.analyzeVariants.R
lib/R/library/HTSeqGenie/unitTests/runit.bamUtils.R
lib/R/library/HTSeqGenie/unitTests/runit.buildGenomicFeatures.R
lib/R/library/HTSeqGenie/unitTests/runit.calculateCoverage.R
lib/R/library/HTSeqGenie/unitTests/runit.checkConfig.R
lib/R/library/HTSeqGenie/unitTests/runit.config.R
lib/R/library/HTSeqGenie/unitTests/runit.detectAdapterContam.R
lib/R/library/HTSeqGenie/unitTests/runit.detectRRNA.R
lib/R/library/HTSeqGenie/unitTests/runit.filterQuality.R
lib/R/library/HTSeqGenie/unitTests/runit.gatk.R
lib/R/library/HTSeqGenie/unitTests/runit.io.R
lib/R/library/HTSeqGenie/unitTests/runit.mergeLanes.R
lib/R/library/HTSeqGenie/unitTests/runit.picard.R
lib/R/library/HTSeqGenie/unitTests/runit.preprocessReads.R
lib/R/library/HTSeqGenie/unitTests/runit.readRNASeqEnds.R
lib/R/library/HTSeqGenie/unitTests/runit.reportPipelineQA.R
lib/R/library/HTSeqGenie/unitTests/runit.runPipeline.R
lib/R/library/HTSeqGenie/unitTests/runit.targetLengths.R
lib/R/library/HTSeqGenie/unitTests/runit.tools.R
lib/R/library/HTSeqGenie/unitTests/runit.trimReads.R
