├── .gitignore ├── README.md ├── adapters ├── NexteraPE-PE.fa ├── TruSeq2-PE.fa ├── TruSeq2-SE.fa ├── TruSeq3-PE-2.fa ├── TruSeq3-PE.fa └── TruSeq3-SE.fa ├── blacklist.rm.sh ├── bowtie2-macs2-homer.smk ├── config.yml ├── data ├── 221RBPs.csv ├── mouse.mm10.excl.bed ├── mouse.mm10.excl.tsv └── mouse.mm9.excl.tsv ├── docker.usage.md ├── envs └── svtools.yaml ├── example ├── dag │ ├── hisat2-stringtie-ballgown.pdf │ ├── hisat2-stringtie-ballgown.png │ ├── rmats.dag.pdf │ ├── rmats.dag.png │ ├── salmon-deseq2-dag.pdf │ └── salmon-deseq2-dag.png ├── fastq │ ├── Sample1_R1.fastq.gz │ ├── Sample1_R2.fastq.gz │ ├── Sample2_R1.fastq.gz │ └── Sample2_R2.fastq.gz └── sample_info_single.txt ├── hisat2-rmats-turbo-v0.1.smk ├── hisat2-rseqc-fastqc-multiqc.smk ├── requirements.txt ├── rules ├── common.smk ├── fastp.smk └── rmats2sashimi.smk ├── salmon-tximport-deseq2-v0.3.smk ├── scripts ├── annotateDEGs.py ├── annotateGenes.R ├── annotateRMATS.py ├── annotateTPMs.py ├── cellnetnp.R ├── collapse_gencode_gtf.py ├── extractGTF.py ├── gseaEnrichr.py ├── gtf2bed.py ├── gtf2pos.infercnv.py ├── inferCNV.R ├── mergeStringTie.py ├── pheatmapDEGs.R ├── run2factorDESeq2.R ├── runBallgown.R ├── runDESeq2.R ├── runDESeq2test.R ├── runDESeq2twofactor.R ├── runTximport.R ├── sex.call.py └── vacanoPlot.R ├── snakeflow-enviroment-setup.sh ├── star-salmon-rmats-v0.1.smk ├── utils ├── blacklist.remove.py ├── boxplot.nofill.py ├── cellranger.custom.build.sh ├── check_md5.sh ├── colormap.py ├── deseq2test.R ├── diffbind.R ├── drawDomains.py ├── draw_protein_domains.py ├── drug_classifier.py ├── getGeneExonLength.sh ├── gitSyncFork.sh ├── igv-webapp.config.py ├── igv.tracks.txt ├── samll_RNA_pipeline.txt ├── step1-trim_glore.sh ├── step1-trimmonatic.sh ├── vimrc.config ├── vocanoplot.and.pearson.correlation.R └── vocanoplot.py └── workflows ├── ATAC.macs3.smk ├── CUTRUN.macs3.smk ├── README.md ├── align.recal.smk ├── amplicon.demuxlet.once.smk ├── amplicon.demuxlet.twice.smk ├── 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