Files in zhangbaifeng/SplitFusion
Detection of gene fusion based on split alignments
.gitignore
DESCRIPTION
NAMESPACE
R/.DS_Store
R/SplitFusion.breakpoint.anno.postscript.R
R/SplitFusion.breakpoint.anno.postscript.direction.R
R/SplitFusion.breakpoint.anno.postscript.direction.sub.R
R/SplitFusion.breakpoint.anno.postscript.mid.anno.R
R/annovar.exon.cds.extraction.R
R/bam2igv.R
R/bed2igv.R
R/build.ensembl.orientation.R
R/fq2png.R
R/runSplitFusion.R
R/snpEff.exon.cds.extraction.R
README.md
SplitFusion.Rproj
example.command.txt
exec/SplitFusion.1_fastq-bam.sh
exec/SplitFusion.2_bam-breakpoint.sh
exec/SplitFusion.3_breakpoint-filter.sh
exec/SplitFusion.4_breakpoint-anno.sh
exec/SplitFusion.py
inst/data/.DS_Store
inst/data/README.md
inst/data/example_data/.DS_Store
inst/data/example_data/Lib001.R1.fq
inst/data/example_data/Lib001.R2.fq
inst/data/example_data/Lib001.consolidated.bam
inst/data/example_data/Lib001.consolidated.bam.bai
inst/data/example_data/kick.start.mode.sh
inst/data/example_data/kick_start_mode_result/Lib001/Lib001.EML4_exon6---ALK_exon20.bam
inst/data/example_data/kick_start_mode_result/Lib001/Lib001.EML4_exon6---ALK_exon20.bam.bai
inst/data/example_data/kick_start_mode_result/Lib001/Lib001.EML4_exon6---ALK_exon20.txt
inst/data/example_data/kick_start_mode_result/Lib001/Lib001.EML4_intronic---ALK_exon20.bam
inst/data/example_data/kick_start_mode_result/Lib001/Lib001.EML4_intronic---ALK_exon20.bam.bai
inst/data/example_data/kick_start_mode_result/Lib001/Lib001.EML4_intronic---ALK_exon20.txt
inst/data/example_data/kick_start_mode_result/Lib001/Lib001.brief.summary
inst/data/example_data/kick_start_mode_result/Lib001/Lib001.consolidated.bam
inst/data/example_data/kick_start_mode_result/Lib001/Lib001.consolidated.bam.bai
inst/data/example_data/kick_start_mode_result/Lib001/Lib001.fusion.list.post-processing.txt
inst/data/example_data/kick_start_mode_result/Lib001/Lib001.fusion.list.pre-processing.txt
inst/data/example_data/kick_start_mode_result/Lib001/Lib001.fusion.table.NoFilter.txt
inst/data/example_data/kick_start_mode_result/Lib001/anno.left.right
inst/data/example_data/kick_start_mode_result/Lib001/anno.mid
inst/data/example_data/kick_start_mode_result/Lib001/breakpoint.candidates
inst/data/example_data/kick_start_mode_result/Lib001/breakpoint.candidates.preFilter
inst/data/example_data/kick_start_mode_result/Lib001/breakpoint.candidates.preFilter.w.mid
inst/data/example_data/kick_start_mode_result/Lib001/breakpoint.siteID.stats.filtered
inst/data/example_data/kick_start_mode_result/Lib001/breakpoint.stats
inst/data/example_data/kick_start_mode_result/Lib001/config.txt
inst/data/example_data/kick_start_mode_result/Lib001/corr.ligat3
inst/data/example_data/kick_start_mode_result/Lib001/header
inst/data/example_data/kick_start_mode_result/Lib001/split.mid
inst/data/example_data/kick_start_mode_result/Lib001/split.mid.expanded
inst/data/example_data/kick_start_mode_result/Lib001/uniq.ligateUmi
inst/data/example_data/normal.mode.sh
inst/data/example_data/normal_mode_result/Lib001/Lib001.EML4_exon6---ALK_exon20.bam
inst/data/example_data/normal_mode_result/Lib001/Lib001.EML4_exon6---ALK_exon20.bam.bai
inst/data/example_data/normal_mode_result/Lib001/Lib001.EML4_exon6---ALK_exon20.txt
inst/data/example_data/normal_mode_result/Lib001/Lib001.EML4_intronic---ALK_exon20.bam
inst/data/example_data/normal_mode_result/Lib001/Lib001.EML4_intronic---ALK_exon20.bam.bai
inst/data/example_data/normal_mode_result/Lib001/Lib001.EML4_intronic---ALK_exon20.txt
inst/data/example_data/normal_mode_result/Lib001/Lib001.brief.summary
inst/data/example_data/normal_mode_result/Lib001/Lib001.consolidated.bam
inst/data/example_data/normal_mode_result/Lib001/Lib001.consolidated.bam.bai
inst/data/example_data/normal_mode_result/Lib001/Lib001.fusion.list.post-processing.txt
inst/data/example_data/normal_mode_result/Lib001/Lib001.fusion.list.pre-processing.txt
inst/data/example_data/normal_mode_result/Lib001/Lib001.fusion.table.NoFilter.txt
inst/data/example_data/normal_mode_result/Lib001/anno.left.right
inst/data/example_data/normal_mode_result/Lib001/anno.mid
inst/data/example_data/normal_mode_result/Lib001/breakpoint.candidates
inst/data/example_data/normal_mode_result/Lib001/breakpoint.candidates.preFilter
inst/data/example_data/normal_mode_result/Lib001/breakpoint.candidates.preFilter.w.mid
inst/data/example_data/normal_mode_result/Lib001/breakpoint.siteID.stats.filtered
inst/data/example_data/normal_mode_result/Lib001/breakpoint.stats
inst/data/example_data/normal_mode_result/Lib001/bwa.log
inst/data/example_data/normal_mode_result/Lib001/config.txt
inst/data/example_data/normal_mode_result/Lib001/corr.ligat3
inst/data/example_data/normal_mode_result/Lib001/header
inst/data/example_data/normal_mode_result/Lib001/split.mid
inst/data/example_data/normal_mode_result/Lib001/split.mid.expanded
inst/data/example_data/normal_mode_result/Lib001/uniq.ligateUmi
inst/data/example_data/sh.nohup.out
inst/data/example_data/specific.step.mode.sh
inst/data/example_data/specific_step_mode_result/Lib001/Lib001.consolidated.bam
inst/data/example_data/specific_step_mode_result/Lib001/Lib001.consolidated.bam.bai
inst/data/example_data/specific_step_mode_result/Lib001/breakpoint.candidates
inst/data/example_data/specific_step_mode_result/Lib001/breakpoint.candidates.preFilter
inst/data/example_data/specific_step_mode_result/Lib001/breakpoint.candidates.preFilter.w.mid
inst/data/example_data/specific_step_mode_result/Lib001/breakpoint.siteID.stats.filtered
inst/data/example_data/specific_step_mode_result/Lib001/breakpoint.stats
inst/data/example_data/specific_step_mode_result/Lib001/bwa.log
inst/data/example_data/specific_step_mode_result/Lib001/config.txt
inst/data/example_data/specific_step_mode_result/Lib001/corr.ligat3
inst/data/example_data/specific_step_mode_result/Lib001/header
inst/data/example_data/specific_step_mode_result/Lib001/split.mid
inst/data/example_data/specific_step_mode_result/Lib001/split.mid.expanded
inst/data/example_data/specific_step_mode_result/Lib001/uniq.ligateUmi
inst/data/example_data/target.mode.sh
inst/data/example_data/target_mode_result/.DS_Store
inst/data/example_data/target_mode_result/Lib001/.DS_Store
inst/data/example_data/target_mode_result/Lib001/Lib001.EML4_exon6---ALK_exon20.bam
inst/data/example_data/target_mode_result/Lib001/Lib001.EML4_exon6---ALK_exon20.bam.bai
inst/data/example_data/target_mode_result/Lib001/Lib001.EML4_exon6---ALK_exon20.txt
inst/data/example_data/target_mode_result/Lib001/Lib001.EML4_intronic---ALK_exon20.bam
inst/data/example_data/target_mode_result/Lib001/Lib001.EML4_intronic---ALK_exon20.bam.2.29446361.svg
inst/data/example_data/target_mode_result/Lib001/Lib001.EML4_intronic---ALK_exon20.bam.2.42492091.svg
inst/data/example_data/target_mode_result/Lib001/Lib001.EML4_intronic---ALK_exon20.bam.bai
inst/data/example_data/target_mode_result/Lib001/Lib001.EML4_intronic---ALK_exon20.txt
inst/data/example_data/target_mode_result/Lib001/Lib001.brief.summary
inst/data/example_data/target_mode_result/Lib001/Lib001.consolidated.bam
inst/data/example_data/target_mode_result/Lib001/Lib001.consolidated.bam.bai
inst/data/example_data/target_mode_result/Lib001/Lib001.fusion.list.post-processing.txt
inst/data/example_data/target_mode_result/Lib001/Lib001.fusion.list.pre-processing.txt
inst/data/example_data/target_mode_result/Lib001/Lib001.fusion.table.NoFilter.txt
inst/data/example_data/target_mode_result/Lib001/anno.left.right
inst/data/example_data/target_mode_result/Lib001/anno.mid
inst/data/example_data/target_mode_result/Lib001/breakpoint.candidates
inst/data/example_data/target_mode_result/Lib001/breakpoint.candidates.preFilter
inst/data/example_data/target_mode_result/Lib001/breakpoint.candidates.preFilter.w.mid
inst/data/example_data/target_mode_result/Lib001/breakpoint.siteID.stats.filtered
inst/data/example_data/target_mode_result/Lib001/breakpoint.stats
inst/data/example_data/target_mode_result/Lib001/bwa.log
inst/data/example_data/target_mode_result/Lib001/config.txt
inst/data/example_data/target_mode_result/Lib001/corr.ligat3
inst/data/example_data/target_mode_result/Lib001/header
inst/data/example_data/target_mode_result/Lib001/split.mid
inst/data/example_data/target_mode_result/Lib001/split.mid.expanded
inst/data/example_data/target_mode_result/Lib001/uniq.ligateUmi
inst/data/panel/LungFusion.GSP2.bed
inst/data/panel/SARC.GSP2.bed
inst/data/panel/filter.gene-gene.txt
inst/data/panel/known.3UTR.truncation.txt
inst/data/panel/known.gene-exon.txt
inst/data/panel/known.gene-gene.txt
inst/data/panel/known.partners.txt
inst/data/refGene.mostExon.NM
inst/data/refGene0.txt
man/AnchoredFusion.breakpoint.anno.postscript.Rd
man/exon.cds.extraction.Rd
man/fq2png.Rd
man/runAnchoredFusion.Rd
man/t
