Snakemake-Workflows
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- cellranger-count Public
A Snakemake workflow for counting single cell RNAseq (scRNA-seq) data with Cell Ranger (Cell Ranger licensing requires a manual download of the software).
snakemake-workflows/cellranger-count’s past year of commit activity - rna-longseq-de-isoform Public
long read differential expression analysis and splice variant analysis
snakemake-workflows/rna-longseq-de-isoform’s past year of commit activity - dna-seq-varlociraptor Public
A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
snakemake-workflows/dna-seq-varlociraptor’s past year of commit activity - rna-seq-kallisto-sleuth Public
A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
snakemake-workflows/rna-seq-kallisto-sleuth’s past year of commit activity - dna-seq-benchmark Public
A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
snakemake-workflows/dna-seq-benchmark’s past year of commit activity - dna-seq-short-read-circle-map Public
A snakemake workflow for calling extrachromosomal circular DNA in Illumina short-read sequencing data with Circle-Map
snakemake-workflows/dna-seq-short-read-circle-map’s past year of commit activity - dna-seq-mtb Public
A flavor of https://github.com/snakemake-workflows/dna-seq-varlociraptor preconfigured for molecular tumor boards
snakemake-workflows/dna-seq-mtb’s past year of commit activity
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