{"payload":{"pageCount":1,"repositories":[{"type":"Public","name":"Alternative-Proteome-Detection-Project","owner":"sheynkman-lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-25T15:09:19.856Z"}},{"type":"Public","name":"biosurfer_analysis","owner":"sheynkman-lab","isFork":false,"description":"This repository reproduces the analysis for biosurfer tool","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-18T18:18:33.400Z"}},{"type":"Public","name":"biosurfer","owner":"sheynkman-lab","isFork":false,"description":"\"Surf\" the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":25,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-15T01:13:06.920Z"}},{"type":"Public","name":"sheynkman-lab-docs","owner":"sheynkman-lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-31T16:31:23.085Z"}},{"type":"Public","name":"pdb-isoform-analysis","owner":"sheynkman-lab","isFork":false,"description":"Comparison of all available PDB chains (human) to the alternative isoforms in GENCODE.","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-12T15:21:16.341Z"}},{"type":"Public","name":"revio-mas-bulk-benchmark","owner":"sheynkman-lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-06T19:48:51.451Z"}},{"type":"Public","name":"sqtl_pipeline_v2","owner":"sheynkman-lab","isFork":true,"description":"Pipeline to map sQTLs to protein isoforms","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-17T16:01:51.213Z"}},{"type":"Public","name":"Coon_isoform_analysis","owner":"sheynkman-lab","isFork":false,"description":"Looking at things related to data from https://www.nature.com/articles/s41587-023-01714-x#Sec24","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-05-04T02:13:39.000Z"}},{"type":"Public","name":"LIME","owner":"sheynkman-lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-16T22:03:13.915Z"}},{"type":"Public","name":"SMC_proteogenomics","owner":"sheynkman-lab","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":"2023-04-07T19:58:43.566Z"}},{"type":"Public","name":"Biosurfer_BMD_analysis","owner":"sheynkman-lab","isFork":false,"description":"This code repository uses the Biosurfer tool (old version) to conduct NMD and protein truncation analysis for long-read bone proteogenomics project.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-13T18:05:18.563Z"}},{"type":"Public template","name":"Long-Read-Proteogenomics","owner":"sheynkman-lab","isFork":false,"description":"A workflow for enhanced protein isoform detection through integration of long-read RNA-seq and mass spectrometry-based proteomics.","allTopics":["nextflow","proteomics","isoforms","long-read-sequencing","pipeline"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":8,"starsCount":37,"forksCount":15,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-18T14:13:00.688Z"}},{"type":"Public","name":"splice-event-to-isoform-pipeline","owner":"sheynkman-lab","isFork":false,"description":"Shay's splice event to isoform integration pipeline","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-02T20:46:13.234Z"}},{"type":"Public","name":"IsoSeq-Nextflow","owner":"sheynkman-lab","isFork":false,"description":"Nextflow implementation of IsoSeq3","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-05-20T18:03:51.538Z"}},{"type":"Public","name":"Huvec-Proteogenomic-Analysis","owner":"sheynkman-lab","isFork":false,"description":"HUVEC analysis analyzing proteogenomic data generated from long-read transcriptomic sequencing and bottom-up mass spec data","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-04-25T20:08:39.422Z"}},{"type":"Public","name":"Long-Read-Proteogenomics-Analysis","owner":"sheynkman-lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":1,"starsCount":3,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-01-30T19:57:17.707Z"}},{"type":"Public","name":"tappAS","owner":"sheynkman-lab","isFork":true,"description":"This repository contains the source code for the tappAS application. See README for details.","allTopics":[],"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-11-01T18:42:36.738Z"}},{"type":"Public","name":"sqanti3-docker","owner":"sheynkman-lab","isFork":true,"description":"A docker image to run SQANTI3","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":5,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-08-04T14:38:04.877Z"}},{"type":"Public","name":"SQANTI3_protein","owner":"sheynkman-lab","isFork":true,"description":"Repository of SQANTI3 tool for Quality Control of Long-Read Defined Transcriptomes","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":43,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-04-16T20:23:05.993Z"}}],"repositoryCount":19,"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"}