sns
Analysis pipelines for genomic sequencing data
File Explorer
- atac.sh
- chip-pairs-peaks.sh
- chip.sh
- rna-rsem.sh
- rna-salmon.sh
- rna-snv.sh
- rna-star-groups-dge.sh
- rna-star.sh
- rrbs.sh
- species.sh
- status.sh
- wes-pairs-cnv.sh
- wes-pairs-snv.sh
- wes.sh
- wgbs.sh
- deseq2-compare.R
- deseq2-pca.R
- dge-deseq2.R
- fix-csv.sh
- fragment-sizes.R
- get-ref.sh
- get-set-setting.sh
- gse-fgsea.R
- join-many.sh
- load-install-packages.R
- plot-heatmap.R
- plot-volcano.R
- quant-merge-salmon.R
- route-header.sh
- test-package.R
- vcf-table.R
- align-bismark.sh
- align-bowtie2-atac.sh
- align-bowtie2-chip.sh
- align-bwa-mem.sh
- align-star.sh
- annot-annovar.sh
- annot-regions-annovar.sh
- bam-dedup-bismark.sh
- bam-dedup-sambamba.sh
- bam-ra-rc-gatk.sh
- bam-splitncigar-gatk.sh
- bigwig-bedtools.sh
- bigwig-deeptools.sh
- cnvs-wes-freec.sh
- fastq-clean.sh
- fastq-trim-trimgalore.sh
- fastq-trim-trimmomatic.sh
- meth-bismark.sh
- nucleosomes-nucleoatac.sh
- peaks-hmmratac.sh
- peaks-macs2.sh
- peaks-macs3-hmmratac.sh
- peaks-macs3.sh
- qc-coverage-gatk.sh
- qc-fastqc.sh
- qc-fastqscreen.sh
- qc-fragment-sizes.sh
- qc-picard-rnaseqmetrics.sh
- qc-target-reads-gatk.sh
- quant-featurecounts.sh
- quant-rsem.sh
- quant-salmon.sh
- snvs-gatk-hc.sh
- snvs-lofreq.sh
- snvs-mutect2.sh
- snvs-strelka.sh
- species-centrifuge.sh
- species-fastqscreen.sh
- .gitignore
- CITATION.cff
- gather-fastqs
- generate-settings
- LICENSE
- README.md
- run
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