{"payload":{"pageCount":2,"repositories":[{"type":"Public","name":"Mammary_gland_aging","owner":"UcarLab","isFork":false,"description":"Mammary gland aging project","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-11T16:11:24.186Z"}},{"type":"Public","name":"ERS-vs-CYT-Islet-Stress-Responses","owner":"UcarLab","isFork":false,"description":"This repository contains scripts used to generate figures in paper titled 'Multi-omic Mapping of Human Pancreatic Islet Endoplasmic Reticulum and Cytokine Stress Responses Provide Type 2 Diabetes Genetic Insights'","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-07T17:30:37.918Z"}},{"type":"Public","name":"ucarlab.github.io","owner":"UcarLab","isFork":true,"description":"The Ucar Lab website","allTopics":[],"primaryLanguage":{"name":"SCSS","color":"#c6538c"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":296,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-17T19:00:47.791Z"}},{"type":"Public","name":"AMULET","owner":"UcarLab","isFork":false,"description":"A count based method for detecting doublets from single nucleus ATAC-seq (snATAC-seq) data.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":11,"starsCount":29,"forksCount":5,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-03T21:39:37.343Z"}},{"type":"Public","name":"Scripts-Tutorials","owner":"UcarLab","isFork":false,"description":"Repository for lab scripts and tutorials.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-11-21T21:39:29.547Z"}},{"type":"Public","name":"mice-aging-project","owner":"UcarLab","isFork":false,"description":"Code for Karakaslar, Katiyar et al., Aging Cell 2023","allTopics":["rna-seq","atac-seq","immune-system","flowcytometry"],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-08-21T13:45:43.429Z"}},{"type":"Public","name":"Covid_19_Scripts","owner":"UcarLab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-08-16T16:42:43.093Z"}},{"type":"Public","name":"CoRE-ATAC","owner":"UcarLab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":4,"starsCount":10,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-03-15T18:44:10.436Z"}},{"type":"Public","name":"snATAC_AlignmentAggregator","owner":"UcarLab","isFork":false,"description":"Aggregates alignments for single cell clusters to apply methods for bulk data. Also adjusts reads for the 9bp overhang.","allTopics":[],"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-09-27T21:17:45.292Z"}},{"type":"Public","name":"GREGORHelper","owner":"UcarLab","isFork":false,"description":"Helper scripts for running multiple GREGOR analyses in parallel.","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-08-26T16:29:20.826Z"}},{"type":"Public","name":"iasva","owner":"UcarLab","isFork":false,"description":"Iteratively Adjusted Surrogate Variable Analysis","allTopics":["transcriptomics","heuristic-algorithm","heterogeneity","single-cell-rna-seq","r","single-cell"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":8,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-08-23T19:59:23.665Z"}},{"type":"Public","name":"OverlapCounter","owner":"UcarLab","isFork":false,"description":"MIT licensed code for counting overlaps from snATAC-seq data.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-06-25T20:06:41.719Z"}},{"type":"Public","name":"MPRA_Khetan","owner":"UcarLab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-06-17T14:49:07.386Z"}},{"type":"Public","name":"PEAS","owner":"UcarLab","isFork":false,"description":"Code repository for PEAS (Predict Enhancers from ATAC-seq), including feature extraction files and easy to use python script for training enhancer models and predicting enhancers using MLP Neural Networks.","allTopics":[],"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":5,"starsCount":9,"forksCount":2,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-01-21T19:42:35.016Z"}},{"type":"Public","name":"QuIN","owner":"UcarLab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"JavaScript","color":"#f1e05a"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-12-17T15:51:55.364Z"}},{"type":"Public","name":"BiFET","owner":"UcarLab","isFork":false,"description":"A robust statistical test for TF footprint data analyses","allTopics":["dnase-seq","r","bioconductor","statistical-tests","atac-seq","transcription-factor-binding","footprinting","chromatin-accessibiity"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":1,"starsCount":2,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-03-11T14:28:17.825Z"}},{"type":"Public","name":"snATACClusteringTools","owner":"UcarLab","isFork":false,"description":"Java methods for processing snATAC-seq data.","allTopics":[],"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-03-06T16:35:46.791Z"}},{"type":"Public","name":"snATACClusteringPipeline","owner":"UcarLab","isFork":false,"description":"Pipeline for obtaining clusters from snATAC-seq data.","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-03-06T16:22:17.750Z"}},{"type":"Public","name":"V-SVA","owner":"UcarLab","isFork":false,"description":"V-SVA: An R Shiny application for detecting and annotating hidden sources of variation in single cell RNA-seq data","allTopics":["visualization","r","transcriptomics","single-cell-rna-seq","shiny","scrna-seq-data","surrogate-variable-analysis","ia-sva"],"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":"2020-03-03T16:02:34.426Z"}},{"type":"Public","name":"SexDimorphismNatureCommunications","owner":"UcarLab","isFork":false,"description":"This is a repository that include the code used for the analyses of PBMC ATAC/RNA/flow cytometry data. ","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":6,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-12-30T20:14:32.487Z"}},{"type":"Public","name":"DoubletNN","owner":"UcarLab","isFork":false,"description":"Classifying single cell doublets by using neural networks on UMIs, and HTO-GMM class labels","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-08-30T17:26:34.546Z"}},{"type":"Public","name":"bncmrk-dblts","owner":"UcarLab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-08-30T16:02:15.808Z"}},{"type":"Public","name":"ATAC-seq","owner":"UcarLab","isFork":true,"description":"ATAC-seq Pipeline in conjunction with Duygu Ucar & Jacques Banchereau Laboratories ","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":7,"license":"Creative Commons Attribution 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-12-27T20:30:02.575Z"}},{"type":"Public","name":"ATAC_seq_mm10","owner":"UcarLab","isFork":false,"description":"ATAC-seq data processing pipeline for mice datasets using mm10 genome","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"Creative Commons Attribution 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-10-01T14:40:29.044Z"}},{"type":"Public","name":"Human-immune-aging-Server","owner":"UcarLab","isFork":false,"description":"human-immune-aging-server [shiny application]","allTopics":["javascript","css","r","html5","shiny-apps","aging"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-09-06T19:41:49.356Z"}},{"type":"Public","name":"DiabetesSubmission","owner":"UcarLab","isFork":false,"description":"Figures and supplementary material for the Diabetes submission.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-09-06T14:51:56.654Z"}},{"type":"Public","name":"PrioritizationAnnotation","owner":"UcarLab","isFork":false,"description":"Annotate sites using ChromHMM states, Broad Domains, Stretch Enhancers and Super Enhancers.","allTopics":[],"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-10-04T15:32:05.575Z"}},{"type":"Public","name":"CellSpecificMLScripts","owner":"UcarLab","isFork":false,"description":"Scripts used in our machine learning analysis of cell-type-specific network features.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-10-04T15:31:47.830Z"}},{"type":"Public","name":"CellSpecificNetworks","owner":"UcarLab","isFork":false,"description":"","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-10-04T15:31:19.730Z"}},{"type":"Public","name":"I-ATAC","owner":"UcarLab","isFork":false,"description":"A standalone software platform for the management and pre-processing of ATAC-seq samples","allTopics":[],"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":1,"starsCount":3,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-10-03T18:57:17.928Z"}}],"repositoryCount":31,"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":"UcarLab repositories"}