{"id":26201861,"url":"https://github.com/dmnfarrell/smallrnaseq","last_synced_at":"2025-04-15T06:01:29.508Z","repository":{"id":24650337,"uuid":"28060318","full_name":"dmnfarrell/smallrnaseq","owner":"dmnfarrell","description":"small rna-seq analysis package","archived":false,"fork":false,"pushed_at":"2022-11-07T23:57:24.000Z","size":8728,"stargazers_count":30,"open_issues_count":6,"forks_count":19,"subscribers_count":4,"default_branch":"master","last_synced_at":"2025-04-13T09:54:59.255Z","etag":null,"topics":["bioinformatics","genomics","mirna","python","rna-seq","sequencing","smallrna"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/dmnfarrell.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGES","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-12-15T22:58:05.000Z","updated_at":"2025-04-09T09:32:51.000Z","dependencies_parsed_at":"2023-01-14T02:15:14.880Z","dependency_job_id":null,"html_url":"https://github.com/dmnfarrell/smallrnaseq","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmnfarrell%2Fsmallrnaseq","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmnfarrell%2Fsmallrnaseq/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmnfarrell%2Fsmallrnaseq/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/dmnfarrell%2Fsmallrnaseq/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/dmnfarrell","download_url":"https://codeload.github.com/dmnfarrell/smallrnaseq/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249016625,"owners_count":21198832,"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","genomics","mirna","python","rna-seq","sequencing","smallrna"],"created_at":"2025-03-12T03:24:04.547Z","updated_at":"2025-04-15T06:01:29.432Z","avatar_url":"https://github.com/dmnfarrell.png","language":"Python","readme":"# smallrnaseq - tool for analysis of small RNA sequencing data\n\n\u003cimg align=\"right\" src=https://raw.githubusercontent.com/dmnfarrell/smallrnaseq/master/img/logo.png width=150px\u003e\n\nsmallrnaseq is a Python package that integrates some of the standard approaches for convenient pre-processing, quantification and analysis of small RNAs. It includes a [command line interface](https://github.com/dmnfarrell/smallrnaseq/wiki/Command-line-interface) used in conjunction with a configuration file. Hence knowledge of Python is not a necessity for using this software. The aim is to provide convenience but with enough configuration to allow some flexibility. Supported on linux and OSX.\n\nFunctionality includes:\n\n* command line interface\n* ability to use several different short read aligners, (currently bowtie or subread)\n* counting of mapped reads to annotated sequences or genomic features\n* counting of miRNAs and isomiRs\n* novel miRNA prediction\n* running multiple files in a batch\n* use of several normalization methods\n\n### Usage\n\nUp to date documentation is at http://smallrnaseq.readthedocs.io\n\nThere is a video tutorial at https://youtu.be/m24cuLyTqg0\n\n### Installation\n\n```pip install smallrnaseq```\n\nor \n\n```pip install -e git+https://github.com/dmnfarrell/smallrnaseq.git#egg=smallrnaseq```\n\nSee the [installation page](http://smallrnaseq.readthedocs.io/en/latest/description.html#installation) for more details \n\n### Python Dependencies\n\n* Numpy\n* Pandas\n* Matplotlib\n* HTSeq\n* Seaborn\n* bx-python\n* scikit-learn\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdmnfarrell%2Fsmallrnaseq","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdmnfarrell%2Fsmallrnaseq","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdmnfarrell%2Fsmallrnaseq/lists"}