{"id":17278241,"url":"https://github.com/saketkc/rna-seq-snakemake","last_synced_at":"2025-10-22T02:57:54.826Z","repository":{"id":141911722,"uuid":"73066250","full_name":"saketkc/rna-seq-snakemake","owner":"saketkc","description":"Snakemake based pipeline for RNA-Seq analysis","archived":false,"fork":false,"pushed_at":"2019-06-26T19:04:00.000Z","size":56,"stargazers_count":31,"open_issues_count":1,"forks_count":12,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-27T22:12:41.402Z","etag":null,"topics":["bioinformatics","pipeline","rna-seq-analysis","rna-seq-snakemake","snakemake"],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-2-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/saketkc.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-11-07T10:13:57.000Z","updated_at":"2023-05-12T03:22:48.000Z","dependencies_parsed_at":null,"dependency_job_id":"ee33949a-1cfc-4535-a7ba-3d2cfd20fcf1","html_url":"https://github.com/saketkc/rna-seq-snakemake","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saketkc%2Frna-seq-snakemake","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saketkc%2Frna-seq-snakemake/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saketkc%2Frna-seq-snakemake/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saketkc%2Frna-seq-snakemake/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saketkc","download_url":"https://codeload.github.com/saketkc/rna-seq-snakemake/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248848660,"owners_count":21171420,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["bioinformatics","pipeline","rna-seq-analysis","rna-seq-snakemake","snakemake"],"created_at":"2024-10-15T09:11:10.318Z","updated_at":"2025-09-16T20:13:11.146Z","avatar_url":"https://github.com/saketkc.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# rna-seq-snakamake\nSnakemake based pipeline for RNA-Seq analysis\n\nInputs to all snakefiles are specified using a `config.py`, and generally is as simple as specifiying the directory\ncontaining all `*.fq/*.fq.gz/*.fastq.gz/*.sra` files.\n\n1. [Snakefile_fastq_multilane.snake](Snakefile_fastq_multilane.snake) - For multilane paired end fastq files\n\n2. [Snakefile_sra_pe](Snakefile_sra_pe) - For paired end `*.sra` files\n\n3. [Snakefile_sra_se](Snakefile_sra_se) - For single end `*.sra` files\n\n4. [Snakefile_fastq](Snakefile_fastq) - For paired end fastq files\n\n## Dependecies\n\n- snakemake\n- STAR\n- bamtools\n- DESeq2\n- qualimap\n- multiqc\n- rseqc\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaketkc%2Frna-seq-snakemake","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaketkc%2Frna-seq-snakemake","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaketkc%2Frna-seq-snakemake/lists"}