{"payload":{"pageCount":2,"repositories":[{"type":"Public","name":"splicekit","owner":"bedapub","isFork":false,"description":"splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":15,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-10T08:48:49.504Z"}},{"type":"Public","name":"bksnake","owner":"bedapub","isFork":false,"description":"Public version of bksnake - biokit snakemake - bulk RNASeq Snakemake workflow","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-04T10:34:06.725Z"}},{"type":"Public","name":"designit","owner":"bedapub","isFork":false,"description":"Blocking and randomization for experimental design","allTopics":["randomization","rstats","design-of-experiments"],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":4,"issueCount":15,"starsCount":7,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-19T14:51:23.322Z"}},{"type":"Public","name":"ComplexSim","owner":"bedapub","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-16T13:18:47.806Z"}},{"type":"Public","name":"HBVouroboros","owner":"bedapub","isFork":false,"description":"HBVouroboros automates sequencing-based HBV genotyping and expression profiling","allTopics":["bioinformatics","snakemake","expression","hbv","genotyping","snakemake-workflow"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":6,"issueCount":5,"starsCount":2,"forksCount":1,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-09T19:36:41.316Z"}},{"type":"Public","name":"ribiosAnnotation","owner":"bedapub","isFork":false,"description":"Annotate features (genes, mRNAs, proteins, ...) with ribios","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":2,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-07T16:02:49.520Z"}},{"type":"Public","name":"besca","owner":"bedapub","isFork":false,"description":"BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":6,"issueCount":26,"starsCount":49,"forksCount":16,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-25T11:05:21.836Z"}},{"type":"Public","name":"ribiosScripts","owner":"bedapub","isFork":false,"description":"Rscripts as command-line tools from the corresponding repository on BEDA github.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-17T08:39:44.322Z"}},{"type":"Public","name":"PMDA-Summer-School","owner":"bedapub","isFork":true,"description":"Public website of Roche PMDA Summer School ","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":3,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-17T08:14:35.646Z"}},{"type":"Public","name":"ribiosUtils","owner":"bedapub","isFork":false,"description":"The ribiosUtils package, a swiss-army knife for bioinformatics and computational biology tasks in drug discovery","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-16T13:31:31.681Z"}},{"type":"Public","name":"GeMS","owner":"bedapub","isFork":false,"description":"Gene set management system based on a MongoDB backend","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":3,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-17T00:23:05.462Z"}},{"type":"Public","name":"MelanomaCITResponse_scRNAseq_TILandPBMC_publication","owner":"bedapub","isFork":false,"description":"This repository includes notebooks utilized to produce results for the publication \"Myeloid-T cell interplay, cell state transitions and checkpoint inhibitor response in melanoma\"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-08T18:11:28.074Z"}},{"type":"Public","name":"CD8-immune-phenotype-paper-supplementary","owner":"bedapub","isFork":false,"description":"Supplementary source code for the CD8 immune phenotype publication","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-01T15:58:01.496Z"}},{"type":"Public","name":"GLOC-hep_distr_and_system_param","owner":"bedapub","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-26T14:34:31.651Z"}},{"type":"Public","name":"kinex","owner":"bedapub","isFork":false,"description":"Kinex infers causal kinases from phosphoproteomics data","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-07T18:58:13.819Z"}},{"type":"Public","name":"ribiosNGS","owner":"bedapub","isFork":false,"description":"Next-generation sequencing data analysis with ribios","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":5,"starsCount":2,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-03T17:03:55.966Z"}},{"type":"Public","name":"refsnake","owner":"bedapub","isFork":false,"description":"Snakemake workflow to generate reference genomes and annotations","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-20T15:34:57.775Z"}},{"type":"Public","name":"dynamic-form","owner":"bedapub","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":2,"issueCount":0,"starsCount":2,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-12T07:20:57.109Z"}},{"type":"Public","name":"cd8ippred","owner":"bedapub","isFork":false,"description":"R package to predict immune phenotypes from RNA-Seq","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-05T14:14:52.036Z"}},{"type":"Public","name":"ribiosPlot","owner":"bedapub","isFork":false,"description":"Data transformation and visualization with the ribios suite","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-01T12:36:16.975Z"}},{"type":"Public","name":"ribiosExpression","owner":"bedapub","isFork":false,"description":"Data structure and functions for gene expression analysis","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-29T15:13:11.863Z"}},{"type":"Public","name":"ngs-tools","owner":"bedapub","isFork":false,"description":"Helper tools written in C, Bash, Python, and R for next-generation sequencing data analysis.","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-14T13:48:30.038Z"}},{"type":"Public","name":"sapiens","owner":"bedapub","isFork":false,"description":"Gene Signature Annotation Pipeline","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-17T14:18:28.445Z"}},{"type":"Public","name":"metadata-registration-api","owner":"bedapub","isFork":false,"description":"A flask microservice to register and manage metadata via an API.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":3,"issueCount":0,"starsCount":1,"forksCount":1,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-01T23:13:53.132Z"}},{"type":"Public","name":"bios-to-go","owner":"bedapub","isFork":false,"description":"Static files of the BIOS, aka Bioinfo-C, library","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"GNU Lesser General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-25T14:58:58.018Z"}},{"type":"Public","name":"BP40087_paper_supplementary_code","owner":"bedapub","isFork":false,"description":"Supplementary source code related to the clinical trial BP40087","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-17T08:14:48.225Z"}},{"type":"Public","name":"microbiome10XVisium","owner":"bedapub","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-13T13:52:17.769Z"}},{"type":"Public","name":"space-microbe","owner":"bedapub","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-10T19:35:00.448Z"}},{"type":"Public","name":"ribiosGSEA","owner":"bedapub","isFork":false,"description":"Functions for gene-set analysis of various kinds supported by ribios","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":3,"starsCount":1,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-29T12:48:31.794Z"}},{"type":"Public","name":"ribiosMath","owner":"bedapub","isFork":false,"description":"Mathematical objects and functions in the ribios software suite","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-27T15:39:10.766Z"}}],"repositoryCount":47,"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":"bedapub repositories"}