{"payload":{"pageCount":3,"repositories":[{"type":"Public","name":"ENVI","owner":"dpeerlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":4,"starsCount":31,"forksCount":3,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-20T17:18:17.517Z"}},{"type":"Public","name":"Palantir","owner":"dpeerlab","isFork":false,"description":"Single cell trajectory detection","topicNames":["markov-chain","dimensionality-reduction","scrna-seq","trajectory-generation","diffusion-maps","differentiation","manifold-learning","single-cell-genomics","cell-fate-transitions","scrna-seq-analysis"],"topicsNotShown":0,"allTopics":["markov-chain","dimensionality-reduction","scrna-seq","trajectory-generation","diffusion-maps","differentiation","manifold-learning","single-cell-genomics","cell-fate-transitions","scrna-seq-analysis"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":3,"starsCount":196,"forksCount":45,"license":"GNU General Public License v2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-15T20:31:07.299Z"}},{"type":"Public","name":"cellpose","owner":"dpeerlab","isFork":true,"description":"a generalist algorithm for cellular segmentation with human-in-the-loop capabilities","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":348,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-13T18:59:23.423Z"}},{"type":"Public","name":"STAR","owner":"dpeerlab","isFork":true,"description":"RNA-seq aligner","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":491,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-10T13:13:44.001Z"}},{"type":"Public","name":"benchkit","owner":"dpeerlab","isFork":false,"description":"Scripts for managing and processing large number of samples, also providing a CLI.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-09T16:22:05.903Z"}},{"type":"Public","name":"SEACells","owner":"dpeerlab","isFork":false,"description":"SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":1,"issueCount":23,"starsCount":136,"forksCount":24,"license":"GNU General Public License v2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-03T20:40:01.941Z"}},{"type":"Public","name":"docker-cellranger","owner":"dpeerlab","isFork":true,"description":"Dockerized Cell Ranger","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":3,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-03T02:23:38.853Z"}},{"type":"Public","name":"WassersteinWormhole","owner":"dpeerlab","isFork":false,"description":"Transformer Based Embeddings of Wasserstein Distance","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":6,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-26T21:59:49.173Z"}},{"type":"Public","name":"ecosystem-packages","owner":"dpeerlab","isFork":true,"description":"Register pe'er lab packages to scverse ecosystem","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":34,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-15T18:40:31.025Z"}},{"type":"Public","name":"spectra","owner":"dpeerlab","isFork":false,"description":"Supervised Pathway DEConvolution of InTerpretable Gene ProgRAms","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":4,"issueCount":15,"starsCount":126,"forksCount":16,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-15T16:45:29.436Z"}},{"type":"Public","name":"mssi","owner":"dpeerlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":1,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-19T18:29:40.156Z"}},{"type":"Public","name":"cytopus","owner":"dpeerlab","isFork":true,"description":"Single cell omics biology annotations","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":2,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-14T19:35:17.338Z"}},{"type":"Public","name":"PrismSpot","owner":"dpeerlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-24T23:19:04.685Z"}},{"type":"Public","name":"scKINETICS","owner":"dpeerlab","isFork":false,"description":"Code for scKINETICS (ISMB 2023)","topicNames":["expectation-maximization","atac-seq","single-cell-analysis","gene-regulatory-network"],"topicsNotShown":0,"allTopics":["expectation-maximization","atac-seq","single-cell-analysis","gene-regulatory-network"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":3,"starsCount":20,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-23T19:18:20.130Z"}},{"type":"Public","name":"scing","owner":"dpeerlab","isFork":true,"description":"SCING: Single-Cell pIpeliNe Garden (pronounced as \"sing\" /siŋ/)","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":3,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-10-05T15:50:01.287Z"}},{"type":"Public","name":"MERlin","owner":"dpeerlab","isFork":true,"description":"MERFISH decoding software","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":1,"forksCount":28,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-19T16:19:29.887Z"}},{"type":"Public","name":"sharp","owner":"dpeerlab","isFork":true,"description":"A single-cell demultiplexing pipeline, the sharp (♯)","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-05T00:04:07.126Z"}},{"type":"Public","name":"Treg_depletion_reproducibility","owner":"dpeerlab","isFork":false,"description":"Code related to analyses in Glasner, Rose, Sharma, et al Nature Immunology 2023. ","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-13T18:51:04.940Z"}},{"type":"Public","name":"SpectraReproducibility","owner":"dpeerlab","isFork":false,"description":"Notebooks for reproducing figures in the Spectra paper","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":2,"starsCount":5,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-07T08:29:38.712Z"}},{"type":"Public","name":"ArchR","owner":"dpeerlab","isFork":true,"description":"ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":126,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-17T18:41:06.153Z"}},{"type":"Public","name":"Harmony","owner":"dpeerlab","isFork":false,"description":"Harmony framework for connecting scRNA-seq data from discrete time points","topicNames":["scrna-seq","mnn","batch-correction","scrna-seq-analysis","developmental-trajecotries"],"topicsNotShown":0,"allTopics":["scrna-seq","mnn","batch-correction","scrna-seq-analysis","developmental-trajecotries"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":6,"starsCount":44,"forksCount":12,"license":"GNU General Public License v2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-12T18:25:26.920Z"}},{"type":"Public","name":"pdac-progression","owner":"dpeerlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":1,"starsCount":9,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-28T02:47:37.534Z"}},{"type":"Public","name":"wdl-cellranger-arc","owner":"dpeerlab","isFork":true,"description":"WDLized Cell Ranger ARC","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"WDL","color":"#42f1f4"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-21T21:33:38.314Z"}},{"type":"Public","name":"wdl-cellranger-gex","owner":"dpeerlab","isFork":true,"description":"WDLized Cell Ranger GEX","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"WDL","color":"#42f1f4"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-11T21:41:31.287Z"}},{"type":"Public","name":"docker-cellranger-arc","owner":"dpeerlab","isFork":true,"description":"Dockerized Cell Ranger ARC","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-04T17:31:47.709Z"}},{"type":"Public","name":"Lineage_Plasticity_in_CRPC","owner":"dpeerlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":7,"forksCount":3,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-15T22:17:28.214Z"}},{"type":"Public","name":"SEACellsReproducibility","owner":"dpeerlab","isFork":false,"description":"Notebooks for reproducing figures in the SEACells manuscript","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-04T17:29:22.179Z"}},{"type":"Public","name":"SpaceFold_paper","owner":"dpeerlab","isFork":false,"description":"The repository contains scripts used in the manuscript.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-10-09T04:14:04.979Z"}},{"type":"Public","name":"SpaceFold","owner":"dpeerlab","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":1,"starsCount":4,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-10-09T04:13:21.996Z"}},{"type":"Public","name":"SCLC_atlas-HTAN","owner":"dpeerlab","isFork":false,"description":"Single-cell atlas of SCLC leveraging scRNA-seq, MIBI, and Vectra imaging, as part of the Human Tumor Atlas Network","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":1,"starsCount":7,"forksCount":6,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-08-30T14:03:07.206Z"}}],"repositoryCount":63,"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"}