{"payload":{"pageCount":3,"repositories":[{"type":"Public","name":"MotifPeeker","owner":"neurogenomics","isFork":false,"description":"Benchmark Epigenomic Profiling Methods with Motif Enrichment as Key Metric","allTopics":["bioconductor","chip-seq","r-package","epigenomics","bioconductor-package","motif-enrichment-analysis","interactive-report"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"GNU General Public License v3.0","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,27,21,11,25,7,2,2,3,8],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-10T16:30:17.170Z"}},{"type":"Public","name":"rworkflows","owner":"neurogenomics","isFork":false,"description":"Continuous integration for R packages. π Automates testing β
, documentation website building π¦, & containerised deployment π³. ","allTopics":["docker","continuous-integration","containers","bioconductor","dockerhub","reproducibility","workflows","cran-r","r","github-actions"],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":2,"issueCount":30,"starsCount":71,"forksCount":7,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-10T16:28:42.228Z"}},{"type":"Public","name":"neurogenomics-lab-website","owner":"neurogenomics","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"TeX","color":"#3D6117"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":4,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-09T08:14:43.127Z"}},{"type":"Public","name":"MungeSumstats","owner":"neurogenomics","isFork":true,"description":"Rapid standardisation and quality control of GWAS or QTL summary statistics","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":15,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-07T13:27:09.432Z"}},{"type":"Public","name":"EnformerCelltyping","owner":"neurogenomics","isFork":false,"description":"Enformer Celltyping is a tensorflow, multi-headed attention based model that incorporates distal effects of Deoxyribonucleic Acid (DNA) interactions to predict histone marks across diverse cell types.","allTopics":[],"primaryLanguage":{"name":"Jupyter Notebook","color":"#DA5B0B"},"pullRequestCount":0,"issueCount":0,"starsCount":5,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-29T10:04:35.843Z"}},{"type":"Public","name":"APOE_microglia","owner":"neurogenomics","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"GNU General Public License v3.0","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,3,0,0,2,0,0,0,3,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-25T13:43:27.804Z"}},{"type":"Public","name":"chromexpress","owner":"neurogenomics","isFork":false,"description":"Which epigenetic factors are the best predictors of gene expression? An analysis using ENCODE data.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":[0,0,0,0,0,0,0,1,0,1,1,0,0,0,4,0,0,0,0,0,2,0,2,0,0,0,0,1,1,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-25T09:06:08.860Z"}},{"type":"Public","name":"rare_disease_celltyping","owner":"neurogenomics","isFork":false,"description":"Code, data and results associated with the \"Rare diseases cell-typing\" project.","allTopics":["genetics","enrichment-analysis","rare-disease","cell-type-deconvolution"],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":5,"starsCount":6,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-24T16:25:09.227Z"}},{"type":"Public","name":"HPOExplorer","owner":"neurogenomics","isFork":false,"description":"Functions for working with the Human Phenotype Ontology data","allTopics":["bioinformatics","genetics","r-package","ontologies","phenome","human-phenotype-ontology","rare-disease","clinical-genomics"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":1,"starsCount":3,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-16T12:38:40.662Z"}},{"type":"Public","name":"MotifPeeker-reports","owner":"neurogenomics","isFork":false,"description":"Public archive of reports generated using MotifPeeker R package","allTopics":["r","database","reproducible-research","epigenomics"],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"GNU General Public License v3.0","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,5,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-16T10:44:16.931Z"}},{"type":"Public","name":"scKirby","owner":"neurogenomics","isFork":false,"description":"Automated ingestion and conversion of various single-cell data formats, within and across species","allTopics":["format-converter","standardization","single-cell-rna-seq","r","r-package"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":1,"issueCount":5,"starsCount":11,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-05T15:16:35.602Z"}},{"type":"Public","name":"MotifStats","owner":"neurogenomics","isFork":false,"description":"Package for integrating peak and motif positions","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-13T09:02:10.490Z"}},{"type":"Public","name":"KGExplorer","owner":"neurogenomics","isFork":false,"description":"Import and analyse large-scale biomedical knowledge graphs and ontologies. πΈοΈβοΈπ»βοΈπΈοΈ","allTopics":["api","bioinformatics","big-data","knowledge-graph","network-analysis","biomedicine"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-11T08:41:20.765Z"}},{"type":"Public","name":"gpt_hpo_annotations","owner":"neurogenomics","isFork":false,"description":"π₯π§ββοΈβ¨π€β¨π¨ββοΈπ₯","allTopics":[],"primaryLanguage":{"name":"JavaScript","color":"#f1e05a"},"pullRequestCount":0,"issueCount":1,"starsCount":1,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-10T15:49:52.642Z"}},{"type":"Public","name":"MAGMA_Celltyping","owner":"neurogenomics","isFork":false,"description":"Find causal cell-types underlying complex trait genetics","allTopics":["gwas","snps","genomics","statistical-genetics","magma","single-cell-omics","single-cell"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":13,"starsCount":69,"forksCount":31,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-17T16:58:37.922Z"}},{"type":"Public","name":"MSTExplorer","owner":"neurogenomics","isFork":false,"description":"Multi-Scale Target Explorer systematically identifies, prioritises, and visualises cell-type-specific gene therapy targets across the phenome.","allTopics":["genetics","parallel-computing","r-package","enrichment-analysis","human-phenotype-ontology","rare-disease","biomedicine","cell-types"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":2,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-06T12:57:46.953Z"}},{"type":"Public","name":"EpiCompare","owner":"neurogenomics","isFork":false,"description":"Comparison, benchmarking & QC of epigenetic datasets","allTopics":["html","benchmarking","benchmark","genetics","comparison","epigenetics","bioconductor","r-package","bioconductor-package","interactive-reporting"],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":15,"starsCount":12,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-04-25T16:08:17.103Z"}},{"type":"Public","name":"ConsensusPeak","owner":"neurogenomics","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":6,"starsCount":0,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-21T11:18:22.384Z"}},{"type":"Public","name":"RareDiseasePrioritisation","owner":"neurogenomics","isFork":false,"description":"Prioritise cell-type-specific gene targets from the Rare Disease Celltyping project.","allTopics":["genomics","scrna-seq","clinical-research","single-cell-genomics","aav","rare-disease","celltypes"],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-21T10:49:05.087Z"}},{"type":"Public","name":"Kayaking","owner":"neurogenomics","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Kotlin","color":"#A97BFF"},"pullRequestCount":0,"issueCount":22,"starsCount":5,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-12T11:45:36.568Z"}},{"type":"Public","name":"labwiki","owner":"neurogenomics","isFork":false,"description":"Tips, intros, and documentation for the Neurogenomics Lab. π§ π§¬","allTopics":["documentation","wiki","collaboration","knowledge-management"],"primaryLanguage":null,"pullRequestCount":0,"issueCount":11,"starsCount":8,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-23T05:55:19.968Z"}},{"type":"Public","name":"scFlow","owner":"neurogenomics","isFork":true,"description":"Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":15,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-02-21T12:18:54.944Z"}},{"type":"Public","name":"rare_disease_celltyping_apps","owner":"neurogenomics","isFork":false,"description":"All apps and homepage code in one place for the rare disease EWCE project. ","allTopics":[],"primaryLanguage":{"name":"CSS","color":"#563d7c"},"pullRequestCount":0,"issueCount":13,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-27T16:29:06.350Z"}},{"type":"Public","name":"Rsamtools","owner":"neurogenomics","isFork":true,"description":"Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":27,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-28T18:17:57.859Z"}},{"type":"Public","name":"orthogene","owner":"neurogenomics","isFork":false,"description":"𧬠o r t h o g e n e π§¬β¨β¨β¨β¨β¨β¨β¨ Interspecies gene mappingβ¨β¨β¨β¨β¨ π¦ π π± π π³ π π π π π πͺ± π πͺ° π π π π¦ π π π π¦ π π π π π π π π π π π π π π π π π 𦧠π π¦ π πββοΈ","allTopics":["bioinformatics","r","genomics","bioconductor","genes","comparative-genomics","r-package","ontologies","evolutionary-biology","bioconductor-package","translational-research","animal-models","biomedicine"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":11,"starsCount":39,"forksCount":4,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-22T05:46:07.735Z"}},{"type":"Public","name":"GenomicRanges","owner":"neurogenomics","isFork":true,"description":"Representation and manipulation of genomic intervals","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":18,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-21T19:22:39.721Z"}},{"type":"Public","name":".github","owner":"neurogenomics","isFork":false,"description":"Neurogenomics Lab Profile","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-12T15:09:27.443Z"}},{"type":"Public template","name":"templateR","owner":"neurogenomics","isFork":false,"description":"Self-updating template for developing R packages.","allTopics":["documentation","r","templates","bioconductor","r-package","cran-r","github-actions"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-09T18:26:33.296Z"}},{"type":"Public","name":"reanalysis_Mathys_2019","owner":"neurogenomics","isFork":false,"description":"A re-analysis of the [Single-cell transcriptomic analysis of Alzheimerβs disease](https://www.nature.com/articles/s41586-019-1195-2) using a standardised data processing and pseudobulk differential expression approach ","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":14,"forksCount":4,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-05T11:56:15.324Z"}},{"type":"Public","name":"ArchR","owner":"neurogenomics","isFork":true,"description":"ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":131,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-11-17T12:01:17.115Z"}}],"repositoryCount":79,"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":"neurogenomics repositories"}