{"payload":{"pageCount":1,"repositories":[{"type":"Public","name":"hic-bench","owner":"NYU-BFX","isFork":false,"description":"A set of pipelines for Hi-C and ChIP-Seq analysis.","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":10,"starsCount":43,"forksCount":20,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-11T13:56:59.369Z"}},{"type":"Public","name":"sns","owner":"NYU-BFX","isFork":true,"description":"illumina sequencing data analysis pipelines","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":26,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-09-23T04:31:56.092Z"}},{"type":"Public","name":"neoantigen-pipeline","owner":"NYU-BFX","isFork":false,"description":"Call somatic mutations and call Class 1 and 2 epitopes ","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-06-02T12:08:13.261Z"}},{"type":"Public","name":"TCGA_downloads","owner":"NYU-BFX","isFork":false,"description":"How to download TCGA data from GDC portal","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-05-03T16:01:18.750Z"}},{"type":"Public","name":"Gene_fusion","owner":"NYU-BFX","isFork":false,"description":"","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-03-30T20:51:14.446Z"}},{"type":"Public","name":"computational-tools","owner":"NYU-BFX","isFork":false,"description":"","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-04-13T04:38:25.744Z"}},{"type":"Public","name":"deep-drug-response","owner":"NYU-BFX","isFork":true,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":10,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-04-18T23:25:52.934Z"}},{"type":"Public","name":"containers","owner":"NYU-BFX","isFork":true,"description":"Docker and Singularity containers for Bioinformatics programs","allTopics":[],"primaryLanguage":{"name":"Dockerfile","color":"#384d54"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":3,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-10-18T14:05:05.218Z"}},{"type":"Public","name":"nf-bio-basic","owner":"NYU-BFX","isFork":true,"description":"Nextflow basic Bioinformatics workflow for testing and demonstration","allTopics":[],"primaryLanguage":{"name":"Makefile","color":"#427819"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":19,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-09-06T20:40:28.593Z"}},{"type":"Public","name":"RNA-Seq_Standard","owner":"NYU-BFX","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":11,"forksCount":13,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-08-03T01:44:28.724Z"}},{"type":"Public","name":"nextflow-demos","owner":"NYU-BFX","isFork":true,"description":"Example Nextflow pipelines and programming techniques","allTopics":[],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":26,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-05-31T12:39:56.716Z"}},{"type":"Public","name":"nextflow-boilerplate","owner":"NYU-BFX","isFork":true,"description":"Boilerplate code for Nextflow pipelines","allTopics":[],"primaryLanguage":{"name":"Nextflow","color":"#3ac486"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-05-08T15:30:48.813Z"}},{"type":"Public","name":"conda-phoenix","owner":"NYU-BFX","isFork":true,"description":"how to set up Anaconda and Conda environments on NYULMC phoenix HPC cluster","allTopics":[],"primaryLanguage":{"name":"Makefile","color":"#427819"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-01-17T01:20:25.848Z"}},{"type":"Public","name":"IGV-snapshot-automator","owner":"NYU-BFX","isFork":true,"description":"Script to automatically create and run IGV snapshot batchscripts","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":49,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-01-04T21:44:23.383Z"}},{"type":"Public","name":"docker2singularity-demo","owner":"NYU-BFX","isFork":true,"description":"A demo for converting Docker images to Singularity images.","allTopics":[],"primaryLanguage":{"name":"Makefile","color":"#427819"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":37,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-01-04T06:24:17.849Z"}},{"type":"Public","name":"reference-annotations","owner":"NYU-BFX","isFork":true,"description":"Makefile for reference annotations for hg19 genes & genomic regions","allTopics":[],"primaryLanguage":{"name":"Makefile","color":"#427819"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-12-22T19:02:21.321Z"}},{"type":"Public","name":"docker-sge","owner":"NYU-BFX","isFork":true,"description":"Dockerfile to build a container with SGE installed","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":17,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-12-08T00:00:41.031Z"}},{"type":"Public","name":"singularity-samtools-demo","owner":"NYU-BFX","isFork":true,"description":"Singularity container for samtools ","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-12-06T22:53:18.495Z"}},{"type":"Public","name":"annotate-peaks","owner":"NYU-BFX","isFork":true,"description":"Scripts for .bed file genomic region annotation with various tools","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-10-11T21:49:46.040Z"}},{"type":"Public","name":"peak-type-summary","owner":"NYU-BFX","isFork":true,"description":"ChIPSeeker genomic region summary plotting and annotation script","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-10-10T00:16:07.313Z"}},{"type":"Public","name":"hic-bench-demo","owner":"NYU-BFX","isFork":true,"description":"Demo dataset & usage for HiC-Bench ChIP-Seq pipeline","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-10-09T23:43:34.915Z"}},{"type":"Public","name":"peaks-report","owner":"NYU-BFX","isFork":true,"description":"A quick report to make a plot & table of the number of peaks per BED file in a dir","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-10-09T15:13:46.254Z"}},{"type":"Public","name":"lncRNA-screen","owner":"NYU-BFX","isFork":false,"description":"lncRNA-screen","allTopics":[],"primaryLanguage":{"name":"Shell","color":"#89e051"},"pullRequestCount":0,"issueCount":1,"starsCount":26,"forksCount":18,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-04-19T16:20:18.090Z"}},{"type":"Public","name":"UCSC-custom-track-generator","owner":"NYU-BFX","isFork":true,"description":"Script to automatically generate custom tracks to load on UCSC","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-04-06T02:27:33.470Z"}},{"type":"Public","name":"AutoReportLite","owner":"NYU-BFX","isFork":true,"description":"Automatic analysis pipline & reporting template","allTopics":[],"primaryLanguage":{"name":"TeX","color":"#3D6117"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-09-27T01:19:59.414Z"}},{"type":"Public","name":"g-content","owner":"NYU-BFX","isFork":false,"description":"Gene content in n-grams, lateral gene transfer detection","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-08-23T22:43:27.892Z"}},{"type":"Public","name":"hic-bench_documentation","owner":"NYU-BFX","isFork":false,"description":"User manuals for the HiC-Bench software","allTopics":[],"primaryLanguage":{"name":"TeX","color":"#3D6117"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2016-04-07T20:14:28.889Z"}}],"repositoryCount":27,"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":"NYU-BFX repositories"}