{"payload":{"pageCount":5,"repositories":[{"type":"Public","name":"splitcode","owner":"pachterlab","isFork":false,"description":"Flexible and efficient parsing, interpreting and editing of sequencing reads","allTopics":[],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":0,"issueCount":12,"starsCount":38,"forksCount":1,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-22T01:49:52.207Z"}},{"type":"Public","name":"kallisto","owner":"pachterlab","isFork":false,"description":"Near-optimal RNA-Seq quantification","allTopics":["rna-seq","kallisto","pseudoalignment"],"primaryLanguage":{"name":"C","color":"#555555"},"pullRequestCount":10,"issueCount":168,"starsCount":648,"forksCount":171,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-22T01:17:14.062Z"}},{"type":"Public","name":"gget","owner":"pachterlab","isFork":false,"description":"🧬 gget enables efficient querying of genomic reference databases","allTopics":["reference","databases","ensembl","blast","uniprot","ncbi","enrichment-analysis","enrichr","alphafold","gget","archs4","alphafold2"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":4,"issueCount":18,"starsCount":922,"forksCount":73,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-22T00:25:32.917Z"}},{"type":"Public","name":"kb_docs","owner":"pachterlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-21T23:49:21.420Z"}},{"type":"Public","name":"monod","owner":"pachterlab","isFork":false,"description":"The Monod package fits CME models to sequencing data.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":29,"forksCount":3,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-20T21:22:35.697Z"}},{"type":"Public","name":"monod_examples","owner":"pachterlab","isFork":false,"description":"Tutorials for the Monod package, which fits CME models to sequencing data.","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":2,"starsCount":6,"forksCount":1,"license":"BSD 2-Clause \"Simplified\" License","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,7,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-20T15:40:14.529Z"}},{"type":"Public","name":"LSCHWCP_2023","owner":"pachterlab","isFork":false,"description":"Identification of viral RNA in single-cell RNA sequencing data","allTopics":["virus","kallisto","translated","viral","palmdb","translated-alignment","comma-free-code"],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":1,"starsCount":1,"forksCount":1,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-20T01:34:48.516Z"}},{"type":"Public","name":"voyager","owner":"pachterlab","isFork":false,"description":"From geospatial to spatial -omics","allTopics":["exploratory-data-analysis","spatial","eda","bioconductor","r-package","omics","transcriptomics","spatial-statistics","esda","spatial-transcriptomics","r","rstats"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":11,"starsCount":70,"forksCount":8,"license":"Artistic License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-19T19:48:35.484Z"}},{"type":"Public","name":"SpatialFeatureExperiment","owner":"pachterlab","isFork":false,"description":"Extension of SpatialExperiment with sf","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":16,"starsCount":36,"forksCount":7,"license":"Artistic License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-19T04:50:34.700Z"}},{"type":"Public","name":"qcbc","owner":"pachterlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":19,"forksCount":3,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-16T21:41:55.491Z"}},{"type":"Public","name":"seqspec","owner":"pachterlab","isFork":false,"description":"machine-readable file format for genomic library sequence and structure","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":3,"starsCount":109,"forksCount":17,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-16T03:41:27.013Z"}},{"type":"Public","name":"SHSOHMP_2024","owner":"pachterlab","isFork":false,"description":"Code for reproducing the results in the second version of the preprint \"Accurate quantification of single-nucleus and single-cell RNA-seq transcripts\"","allTopics":[],"primaryLanguage":{"name":"C++","color":"#f34b7d"},"pullRequestCount":0,"issueCount":0,"starsCount":5,"forksCount":1,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-15T18:40:36.546Z"}},{"type":"Public","name":"HSSHMP_2024","owner":"pachterlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-13T19:19:32.963Z"}},{"type":"Public","name":"LSRRSRLFKOTWMWMP_2024","owner":"pachterlab","isFork":false,"description":"Repository for reproducing results for lr-kallisto ","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":5,"forksCount":1,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-12T20:08:30.361Z"}},{"type":"Public","name":"concordex","owner":"pachterlab","isFork":false,"description":"Identification of spatial homogeneous regions","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":17,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-10T22:57:31.512Z"}},{"type":"Public","name":"concordexR","owner":"pachterlab","isFork":false,"description":"Compute the neighborhood consolidation matrix and identify SHRs","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":10,"forksCount":0,"license":"Artistic License 2.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-08T23:12:11.127Z"}},{"type":"Public","name":"CGCCP_2023","owner":"pachterlab","isFork":false,"description":"scVI extension for unspliced RNA","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":2,"starsCount":16,"forksCount":1,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-08T22:22:08.142Z"}},{"type":"Public","name":"LP_2024","owner":"pachterlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":5,"forksCount":0,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-05T23:50:00.981Z"}},{"type":"Public","name":"pachterlab.github.io","owner":"pachterlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-03T23:02:44.642Z"}},{"type":"Public","name":"kb_python","owner":"pachterlab","isFork":false,"description":"A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing","allTopics":["scrna-seq","single-cell-rna-seq","rna-velocity-estimation","kallisto","bustools","kb-python"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":1,"issueCount":4,"starsCount":145,"forksCount":23,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-02T16:45:32.352Z"}},{"type":"Public","name":"FGP_2024","owner":"pachterlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":2,"starsCount":4,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-26T18:31:28.935Z"}},{"type":"Public","name":"Chronocell","owner":"pachterlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-26T17:59:17.521Z"}},{"type":"Public","name":"ffq","owner":"pachterlab","isFork":false,"description":"A tool to find sequencing data and metadata from public databases.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":3,"issueCount":0,"starsCount":541,"forksCount":47,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-13T07:42:11.562Z"}},{"type":"Public","name":"CGP_2023","owner":"pachterlab","isFork":false,"description":"Repository for meK-Means Inference Method","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-07T06:29:15.105Z"}},{"type":"Public","name":"FGP_2023","owner":"pachterlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-31T21:20:36.354Z"}},{"type":"Public","name":".github","owner":"pachterlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":null,"pullRequestCount":1,"issueCount":0,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-30T00:31:57.604Z"}},{"type":"Public","name":"biophysics","owner":"pachterlab","isFork":false,"description":"Repository for Pachter Lab Biophysics","allTopics":["dynamics","transcription","single-cell","rna-seq-analysis","biophysics","cme","stochastic-modeling"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":6,"forksCount":0,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-25T18:27:29.446Z"}},{"type":"Public","name":"JBMMCKP_2023","owner":"pachterlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":5,"forksCount":1,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-24T19:10:11.205Z"}},{"type":"Public","name":"picasso","owner":"pachterlab","isFork":false,"description":"Picasso: a methods for embedding points in 2D in a way that respects distances while fitting a user-specified shape.","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":69,"forksCount":7,"license":"BSD 2-Clause \"Simplified\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-15T20:48:48.650Z"}},{"type":"Public","name":"splitcode-tutorial","owner":"pachterlab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-13T00:10:54.090Z"}}],"repositoryCount":132,"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":"pachterlab repositories"}