{"payload":{"pageCount":2,"repositories":[{"type":"Public","name":"CRISPR-millipede-target","owner":"pinellolab","isFork":false,"description":"Calculate the enrichment scores of CRISPR alleles and variants from direct target amplicon-sequencing data using Bayesian linear regression model \"millipede\".","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-19T17:44:02.743Z"}},{"type":"Public","name":"CRISPRme","owner":"pinellolab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":5,"starsCount":17,"forksCount":8,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-19T14:08:51.657Z"}},{"type":"Public","name":"pyrovelocity","owner":"pinellolab","isFork":false,"description":"𝒫robabilistic modeling of RNA velocity ⬱","allTopics":["probabilistic-programming","transcriptomics","pyro","probabilistic-models","single-cell-genomics","single-cell-rna-seq","rna-velocity-estimation","multiomics","deep-generative-model","developmental-trajectories","rna-velocity","rna-splicing","single-cell-multiomics","cell-fate-determination","rna-splicing-analysis"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":19,"issueCount":11,"starsCount":40,"forksCount":5,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-18T20:37:53.944Z"}},{"type":"Public","name":"CRISPR-Correct","owner":"pinellolab","isFork":false,"description":"Perform CRISPR guide mapping and analysis that considers protospace self-editing and surrogate sensor sequences. Self-editing aware mapping takes a hamming-distance approach unbiased by expectations in editing patterns.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":2,"starsCount":1,"forksCount":0,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-18T18:25:15.134Z"}},{"type":"Public","name":"DNA-Diffusion","owner":"pinellolab","isFork":false,"description":"🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨 ","allTopics":["deep-learning","genomics","generative-model","diffusion-models","regulatory-genomics","stable-diffusion","diffusion-probabilistic-models"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":11,"issueCount":8,"starsCount":358,"forksCount":50,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-18T11:03:37.193Z"}},{"type":"Public","name":"CRISPResso2","owner":"pinellolab","isFork":false,"description":"Analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments","allTopics":["quantification","genome-editing","amplicon-sequences"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":4,"issueCount":29,"starsCount":269,"forksCount":93,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-17T04:27:56.730Z"}},{"type":"Public","name":"EPInformer","owner":"pinellolab","isFork":false,"description":"code to run EPInformer for gene expression prediction and gene-enhancer links prioritization ","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":22,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-15T08:57:10.098Z"}},{"type":"Public","name":"CRISPR-CLEAR-data","owner":"pinellolab","isFork":false,"description":"Notebooks used to generate the figures and analyses in CRISPR-CLEAR manuscript.","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-09T18:12:42.857Z"}},{"type":"Public","name":"CRISPR-SURF","owner":"pinellolab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":4,"starsCount":15,"forksCount":3,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-04T17:18:35.033Z"}},{"type":"Public","name":"CRISPR-millipede-helper","owner":"pinellolab","isFork":false,"description":"Helper utility function for running CRISPR-millipede pipelines","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-29T21:06:10.209Z"}},{"type":"Public","name":"GRAFIMO","owner":"pinellolab","isFork":false,"description":"GRAph-based Finding of Individual Motif Occurrences","allTopics":["bioinformatics","motif-scanning","haplotype-aware","genome-variation-graphs","genomic-variants"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":27,"forksCount":2,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-29T15:47:55.316Z"}},{"type":"Public","name":"crispr-bean","owner":"pinellolab","isFork":false,"description":"Base Editing screens' Activity-Normalized variant effect size estimation","allTopics":["screen","bayesian-network","crispr","probabilistic-programming-language","base-editing","count-data-modeling","ngs-sequencing-data"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":1,"starsCount":8,"forksCount":1,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-29T14:37:12.011Z"}},{"type":"Public","name":"dictys","owner":"pinellolab","isFork":false,"description":"Context specific and dynamic gene regulatory network reconstruction and analysis","allTopics":["network-inference","network-visualization","network-analysis","single-cell-analysis","gene-regulatory-network","dynamic-network","single-cell-multiomics","single-cell-network"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":108,"forksCount":14,"license":"GNU Affero General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-27T21:24:24.105Z"}},{"type":"Public","name":"ACCESS-ATAC-seq","owner":"pinellolab","isFork":false,"description":"Scripts for ACCESS-ATAC-seq data","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-23T17:38:46.341Z"}},{"type":"Public","name":"screen-simulation","owner":"pinellolab","isFork":false,"description":"Simulate bulk CRISPR screen, sorting or proliferation, with and reproter/target edits","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-15T20:58:27.074Z"}},{"type":"Public","name":"SVG_Benchmarking","owner":"pinellolab","isFork":false,"description":"Benchmarking methods for identification of spatially variable genes","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":1,"issueCount":4,"starsCount":3,"forksCount":2,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-12T14:35:09.808Z"}},{"type":"Public","name":"CRISPR_comparison","owner":"pinellolab","isFork":true,"description":"Snakemake workflow for comparing E-G links to experimental data","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-06T23:16:36.472Z"}},{"type":"Public","name":"ABC-Enhancer-Gene-Prediction","owner":"pinellolab","isFork":true,"description":"Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":59,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-08T22:19:44.654Z"}},{"type":"Public","name":"perturb-tools","owner":"pinellolab","isFork":false,"description":"Analysis Framework for Pooled CRISPR Genome Editing Screens","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-02T18:40:40.941Z"}},{"type":"Public","name":"CRISPR-millipede-pipelines","owner":"pinellolab","isFork":false,"description":"Repository contains the pipeline scripts and resources for running tools in the CRISPR-millipede suite at scale.","allTopics":[],"primaryLanguage":{"name":"WDL","color":"#42f1f4"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-13T18:21:16.226Z"}},{"type":"Public","name":"Xeno-share","owner":"pinellolab","isFork":false,"description":"Script for xenograft SHARE-seq data","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-07T17:30:15.633Z"}},{"type":"Public","name":"scvelo","owner":"pinellolab","isFork":true,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":102,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-01T02:09:39.691Z"}},{"type":"Public","name":"STREAM2_tutorials","owner":"pinellolab","isFork":false,"description":"Tutorials for STREAM2 <a href=\"https://github.com/pinellolab/STREAM2\">https://github.com/pinellolab/STREAM2</a>","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-23T22:48:25.605Z"}},{"type":"Public","name":"AmpUMI","owner":"pinellolab","isFork":false,"description":"Toolkit for the design and analysis of amplicon sequencing experiments utilizing unique molecular identifiers (UMIs)","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":40,"forksCount":8,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-07T17:24:10.020Z"}},{"type":"Public","name":"CRISPRitz","owner":"pinellolab","isFork":false,"description":"Tool package to perform in-silico CRISPR analysis and assessment","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":20,"forksCount":9,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-03T13:28:39.986Z"}},{"type":"Public","name":"bean_manuscript","owner":"pinellolab","isFork":false,"description":"Scripts for plots used in manuscript","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-25T02:53:38.969Z"}},{"type":"Public","name":"CRISPRlungo","owner":"pinellolab","isFork":false,"description":"Genome Editing Analysis of Long UNidirectional sequencing for GenOme Rearrangements","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":5,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-22T23:25:10.868Z"}},{"type":"Public","name":"STREAM2","owner":"pinellolab","isFork":false,"description":"STREAM2: Fast, scalable, and interactive trajectory analysis of single-cell omics data","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":3,"starsCount":8,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-01T17:31:36.359Z"}},{"type":"Public","name":"openproblems-v2","owner":"pinellolab","isFork":true,"description":"Formalizing and benchmarking open problems in single-cell genomics","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":19,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-06T04:48:49.717Z"}},{"type":"Public","name":"simstpy","owner":"pinellolab","isFork":false,"description":"A framework for simulation of spatially-resolved omics data using python","allTopics":["rna-seq","simulation","spatial","atac-seq","multi-omics","cite-seq","cut-tag-seq"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-22T06:16:47.908Z"}}],"repositoryCount":53,"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":"pinellolab repositories"}