{"payload":{"pageCount":2,"repositories":[{"type":"Public","name":"clipnet","owner":"Danko-Lab","isFork":false,"description":"A deep learning approach to predicting transcription initiation from sequence at single nucleotide resolution","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":7,"forksCount":0,"license":"MIT License","participation":[0,0,0,0,0,0,0,4,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,62,67,2,3,9,4,6,2,8,14,35,29,1,2,0,2,8,3,15],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-31T18:39:17.845Z"}},{"type":"Public","name":"clipnet_paper","owner":"Danko-Lab","isFork":false,"description":"Scripts and notebooks to reproduce figures used in the CLIPNET paper","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"MIT License","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,20,44,0,4,0,1,4,0,0,0,0,0,0,1,0,0,1],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-31T15:03:23.556Z"}},{"type":"Public","name":"GLIMPSE2_setup","owner":"Danko-Lab","isFork":false,"description":"Scripts to create a phased reference panel from 1kGP for imputation with GLIMPSE","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":0,"starsCount":1,"forksCount":1,"license":"MIT License","participation":[0,0,0,11,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-22T19:30:09.011Z"}},{"type":"Public","name":"ChRO-seq_paper_data","owner":"Danko-Lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-17T16:41:21.057Z"}},{"type":"Public","name":"proseq2.0","owner":"Danko-Lab","isFork":false,"description":"Preprocesses and Aligns Run-On Sequencing (PRO/GRO/ChRO-seq) data from Single-Read or Paired-End Illumina Sequencing","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":1,"issueCount":6,"starsCount":22,"forksCount":11,"license":"BSD 2-Clause \"Simplified\" License","participation":[1,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-01T08:35:19.454Z"}},{"type":"Public","name":"BayesPrism","owner":"Danko-Lab","isFork":false,"description":"A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":57,"starsCount":127,"forksCount":41,"license":null,"participation":[0,0,0,0,3,0,0,1,3,0,0,0,0,0,0,0,1,0,0,0,5,0,0,0,0,0,0,3,0,0,0,0,0,0,0,1,0,10,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-20T17:09:32.731Z"}},{"type":"Public","name":"dREG","owner":"Danko-Lab","isFork":false,"description":"Detecting Regulatory Elements using GRO-seq and PRO-seq","allTopics":["gene-regulation","pro-seq","chro-seq","transcription-regulatory-elements","gro-seq"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":8,"starsCount":31,"forksCount":21,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-16T21:45:42.301Z"}},{"type":"Public","name":"PROseq_Shapes","owner":"Danko-Lab","isFork":false,"description":"Use the patterns (shapes) within PRO-seq signal to call transcription element annotations","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,7,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-14T20:15:23.389Z"}},{"type":"Public","name":"histone-mark-imputation","owner":"Danko-Lab","isFork":false,"description":"Repo for the histone imputation project.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":3,"starsCount":10,"forksCount":3,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-07T19:35:41.298Z"}},{"type":"Public","name":"E-P_contacts","owner":"Danko-Lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-15T17:44:53.867Z"}},{"type":"Public","name":"RunOnBamToBigWig","owner":"Danko-Lab","isFork":false,"description":" Takes bam files from Run-On sequencing data as input and writes bigWig files as output.","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":4,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-13T19:17:59.563Z"}},{"type":"Public","name":"Danko-Lab.github.io","owner":"Danko-Lab","isFork":false,"description":"Danko lab website","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":2,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-30T18:39:50.799Z"}},{"type":"Public","name":"Prophase-I-Transcription-Project","owner":"Danko-Lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-09T20:44:28.430Z"}},{"type":"Public","name":"tfTarget","owner":"Danko-Lab","isFork":false,"description":"Identify transcription factor-enhancer/promoter-gene network from run-on sequencing data","allTopics":["transcriptional-regulatory-network","enhancer-prediction","pro-seq","chro-seq"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":2,"issueCount":1,"starsCount":7,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-08-27T15:29:18.880Z"}},{"type":"Public","name":"TED","owner":"Danko-Lab","isFork":false,"description":"a fully Bayesian approach to deconvolve tumor microenvironment","allTopics":["scrna-seq","deconvolution","bulk-rna-seq","tumor-cells","stromal-cells","expression-profile","tumor-expression"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":12,"starsCount":60,"forksCount":10,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-06-20T16:11:05.484Z"}},{"type":"Public","name":"dREG-Model","owner":"Danko-Lab","isFork":false,"description":"Models used for running dREG","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-10-11T08:34:37.693Z"}},{"type":"Public","name":"dTOX","owner":"Danko-Lab","isFork":false,"description":"Identification of transcription factor binding patterns using genome-wide accessibility and transcription","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"GNU Lesser General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-10-09T07:30:57.987Z"}},{"type":"Public","name":"ANTXR2","owner":"Danko-Lab","isFork":false,"description":"Analyses for Choate et al.","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-08-09T18:41:02.425Z"}},{"type":"Public","name":"Rgtsvm","owner":"Danko-Lab","isFork":false,"description":"The R package for SVM with GPU architecture based on the GTSVM software","allTopics":["r","svr","e1071-compatibility","gpu","svm","gt-svm","gpu-architecture"],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":12,"starsCount":31,"forksCount":12,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-08-04T16:39:40.233Z"}},{"type":"Public","name":"F1_8Organs","owner":"Danko-Lab","isFork":false,"description":"Genetic Dissection of the RNA Polymerase II Transcription Cycle with ChRO-seq from F1 hybrid mice","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-05-10T03:46:09.016Z"}},{"type":"Public","name":"utils","owner":"Danko-Lab","isFork":false,"description":"General utilities/ convenience scripts useful for munging genomic data.","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":8,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-08-04T21:25:03.777Z"}},{"type":"Public","name":"stabilityHMM","owner":"Danko-Lab","isFork":false,"description":"Inference of transcript stability from polyA and 5' splice site sequence elements","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-06-10T15:55:07.080Z"}},{"type":"Public","name":"polymeraseWaves","owner":"Danko-Lab","isFork":false,"description":"Identifies Pol II 'waves' in GRO-seq or PRO-seq with support for bigWig files.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":1,"issueCount":0,"starsCount":0,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-04-21T13:15:08.687Z"}},{"type":"Public","name":"airavata-php-gateway","owner":"Danko-Lab","isFork":true,"description":"Mirror of Apache Airavata PHP Gateway","allTopics":[],"primaryLanguage":{"name":"PHP","color":"#4F5D95"},"pullRequestCount":1,"issueCount":0,"starsCount":0,"forksCount":38,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-03-27T20:29:09.923Z"}},{"type":"Public","name":"bigWig2","owner":"Danko-Lab","isFork":false,"description":"The extension for the bigWig package in (<a href=\"https://github.com/andrelmartins/bigWig\">https://github.com/andrelmartins/bigWig</a>)","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-03-22T01:20:51.944Z"}},{"type":"Public","name":"HiContactCaller","owner":"Danko-Lab","isFork":false,"description":"Latest version of the contact caller should be updated here","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-01-24T18:55:49.369Z"}},{"type":"Public","name":"AlleleHMM","owner":"Danko-Lab","isFork":false,"description":"A data-driven method to identify allele-specific differences in distributed functional genomic marks","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":5,"forksCount":0,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-10-09T14:57:06.074Z"}},{"type":"Public","name":"HS_transcription_regulation","owner":"Danko-Lab","isFork":false,"description":"Heat shock driven transcription regulation correlated with underlying 3D chromatin contacts","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-09-16T19:37:32.827Z"}},{"type":"Public","name":"Hi-C_contact_caller","owner":"Danko-Lab","isFork":false,"description":"Program for determining the significance of interactions for pairs of points within a chromosome, using a Hi-C contact map","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-07-03T22:01:49.945Z"}},{"type":"Public","name":"LSC-PD_analysis_pipeline","owner":"Danko-Lab","isFork":false,"description":"Pipeline for locus-specific xlinking pull-down analysis","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-05-20T19:10:10.892Z"}}],"repositoryCount":40,"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"}