{"payload":{"pageCount":1,"repositories":[{"type":"Public","name":"dna-seq-benchmark","owner":"snakemake-workflows","isFork":false,"description":"A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":10,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-31T16:01:04.678Z"}},{"type":"Public","name":"dna-seq-varlociraptor","owner":"snakemake-workflows","isFork":false,"description":"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.","allTopics":["snakemake","reproducibility","sciworkflows","genomic-variant-calling","varlociraptor"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":13,"issueCount":6,"starsCount":81,"forksCount":35,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T15:07:03.711Z"}},{"type":"Public","name":"rna-seq-kallisto-sleuth","owner":"snakemake-workflows","isFork":false,"description":"A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.","allTopics":["rna-seq","snakemake","reproducibility","differential-expression","sciworkflows","kallisto","sleuth"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":6,"issueCount":6,"starsCount":63,"forksCount":43,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T10:15:47.744Z"}},{"type":"Public","name":"dna-seq-mtb","owner":"snakemake-workflows","isFork":false,"description":"A flavor of <a href=\"https://github.com/snakemake-workflows/dna-seq-varlociraptor\">https://github.com/snakemake-workflows/dna-seq-varlociraptor</a> preconfigured for molecular tumor boards","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":4,"forksCount":2,"license":"MIT License","participation":[0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,2,2,0,3,0,0,0,0,0,1,0,0,2],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-24T06:29:35.929Z"}},{"type":"Public","name":"transcriptome-differential-expression","owner":"snakemake-workflows","isFork":false,"description":"long read differential expression analysis","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":10,"starsCount":0,"forksCount":0,"license":"Mozilla Public License 2.0","participation":[0,0,0,0,0,0,17,0,0,0,0,0,0,0,0,0,13,9,10,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,5,8,1,1,0,1,0,0,3,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-08T13:56:38.812Z"}},{"type":"Public","name":"dna-seq-short-read-circle-map","owner":"snakemake-workflows","isFork":false,"description":"A snakemake workflow for calling extrachromosomal circular DNA in Illumina short-read sequencing data with Circle-Map","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-03T09:02:04.904Z"}},{"type":"Public","name":"cyrcular-calling","owner":"snakemake-workflows","isFork":false,"description":"A Snakemake workflow for ecDNA detection in Nanopore or Illumina sequencing reads derived from DNA samples enriched for circular DNA.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":6,"starsCount":3,"forksCount":2,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-08T09:44:04.869Z"}},{"type":"Public","name":"rna-seq-star-deseq2","owner":"snakemake-workflows","isFork":false,"description":"RNA-seq workflow using STAR and DESeq2","allTopics":["reproducibility","sciworkflows","gene-expression-analysis","snakemake","deseq2"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":313,"forksCount":191,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-25T20:37:25.185Z"}},{"type":"Public","name":"dna-seq-neoantigen-prediction","owner":"snakemake-workflows","isFork":false,"description":"Snakemake workflow for neoantigen prediction","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":8,"starsCount":14,"forksCount":6,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-07T09:17:09.700Z"}},{"type":"Public template","name":"snakemake-workflow-template","owner":"snakemake-workflows","isFork":false,"description":"A template for standard compliant snakemake-workflows","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":2,"starsCount":78,"forksCount":26,"license":"MIT License","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-18T11:46:20.160Z"}},{"type":"Public","name":"dna-seq-gatk-variant-calling","owner":"snakemake-workflows","isFork":false,"description":"This Snakemake pipeline implements the GATK best-practices workflow","allTopics":["snakemake","gatk","reproducibility","sciworkflows","genomic-variant-calling"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":3,"issueCount":17,"starsCount":234,"forksCount":141,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-08T08:59:18.258Z"}},{"type":"Public","name":"ngs-test-data","owner":"snakemake-workflows","isFork":false,"description":"A workflow for creating small NGS test data sets, useful for continuous integration.","allTopics":["snakemake","ngs","snakemake-workflows"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":2,"issueCount":1,"starsCount":21,"forksCount":14,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-19T16:07:10.119Z"}},{"type":"Public","name":"structure-based-screening","owner":"snakemake-workflows","isFork":false,"description":"Workflow for screening massive amounts of small molecules (ligands) against a target (PDB-File)","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-09T07:46:19.783Z"}},{"type":"Public template","name":"single-cell-drop-seq","owner":"snakemake-workflows","isFork":true,"description":"A SingleCell RNASeq pre-processing pipeline built on snakemake","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":12,"forksCount":46,"license":"Creative Commons Attribution Share Alike 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-11T21:11:36.248Z"}},{"type":"Public template","name":"single-cell-rna-seq","owner":"snakemake-workflows","isFork":false,"description":"A single cell RNA-seq workflow, including highly variable gene analysis, cell type assignment and differential expression analysis.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":1,"issueCount":2,"starsCount":96,"forksCount":42,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-22T23:36:06.748Z"}},{"type":"Public","name":"chipseq","owner":"snakemake-workflows","isFork":false,"description":"ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at <a href=\"https://nf-co.re/chipseq\" rel=\"nofollow\">https://nf-co.re/chipseq</a>).","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":25,"forksCount":18,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-02-03T23:49:50.894Z"}},{"type":"Public","name":"cookiecutter-snakemake-workflow","owner":"snakemake-workflows","isFork":false,"description":"A cookiecutter template for Snakemake workflows","allTopics":["snakemake","snakemake-workflows","cookiecutter-template"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":55,"forksCount":37,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-02-02T18:22:28.828Z"}},{"type":"Public","name":"docs","owner":"snakemake-workflows","isFork":false,"description":"Documentation of the Snakemake-Workflows project","allTopics":["snakemake","snakemake-workflows"],"primaryLanguage":null,"pullRequestCount":0,"issueCount":4,"starsCount":151,"forksCount":24,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-02-02T18:22:06.283Z"}},{"type":"Public","name":"species-quantification","owner":"snakemake-workflows","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-09-06T13:14:03.823Z"}},{"type":"Public","name":"cite-seq-alevin-fry-seurat","owner":"snakemake-workflows","isFork":false,"description":"Snakemake workflow for CITE-seq analaysis with alevin-fry and seurat","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-05-27T15:39:20.447Z"}},{"type":"Public","name":"rad-seq-stacks","owner":"snakemake-workflows","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":8,"starsCount":1,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-01-14T15:57:40.218Z"}},{"type":"Public template","name":"accel-amplicon-trimming","owner":"snakemake-workflows","isFork":true,"description":"Snakemake workflow implementing Accel Amplicon (Swift) trimming guidelines.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":3,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-05-18T11:36:45.370Z"}}],"repositoryCount":22,"userInfo":null,"searchable":true,"definitions":[],"typeFilters":[{"id":"all","text":"All"},{"id":"public","text":"Public"},{"id":"source","text":"Sources"},{"id":"fork","text":"Forks"},{"id":"archived","text":"Archived"},{"id":"template","text":"Templates"}],"compactMode":false},"title":"Repositories"}