{"payload":{"pageCount":2,"repositories":[{"type":"Public","name":"spatialGE.Preprocessing","owner":"genepattern","isFork":false,"description":"Repo for the GenePattern Preprocessing module based on https://github.com/FridleyLab/spatialGE","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-07-02T19:49:07.703Z"}},{"type":"Public","name":"spatialGE.STenrich","owner":"genepattern","isFork":false,"description":"Spatial enrichment of gene sets based on https://github.com/FridleyLab/spatialGE ","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-06-28T21:29:12.531Z"}},{"type":"Public","name":"Harmony","owner":"genepattern","isFork":false,"description":"Wrapper Script for Harmony designed to work with GenePattern Module Integrator","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-29T19:26:25.760Z"}},{"type":"Public","name":"tximport.DESeq2","owner":"genepattern","isFork":true,"description":"tximport.DESeq2 wrapper module for GenePattern.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-04T19:39:30.141Z"}},{"type":"Public","name":"ComBat_Seq","owner":"genepattern","isFork":false,"description":"Batch effect adjustment based on negative binomial regression for RNA sequencing count data. Credits: https://github.com/zhangyuqing/ComBat-seq","allTopics":["negative-binomial-regression","batch-effects","genepattern-module","rna-seq"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-05T21:48:19.946Z"}},{"type":"Public","name":"ComBat","owner":"genepattern","isFork":false,"description":"Performs batch correction on a dataset containing multiple batches","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-05T21:13:49.157Z"}},{"type":"Public","name":"OutSplice.plotJunctions","owner":"genepattern","isFork":false,"description":"Post-processing generation of additional plots from OutSplice runs using the plotJunctionData function","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-03T19:08:51.681Z"}},{"type":"Public","name":"OutSplice","owner":"genepattern","isFork":false,"description":"GenePattern wrapper for https://github.com/GuoLabUCSD/OutSplice","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-03T18:55:03.953Z"}},{"type":"Public","name":"TCGA.SampleSelection","owner":"genepattern","isFork":false,"description":"TCGA.SampleSelection wrapper module for GenePattern.","allTopics":["utilities","tcga","preprocess","msigdb","genepattern-module"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-03T18:02:45.309Z"}},{"type":"Public","name":"CoxRegression","owner":"genepattern","isFork":false,"description":"Cox regression using clinical data and .cls file","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-03T17:13:16.762Z"}},{"type":"Public","name":"NearestTemplatePrediction","owner":"genepattern","isFork":false,"description":"Nearest neighbor prediction based on a list of marker genes","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":7,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-20T19:28:25.723Z"}},{"type":"Public","name":"DESeq2","owner":"genepattern","isFork":false,"description":"A Differential Expression workflow for RNA-Seq data based on the DESeq2 package from Bioconductor","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":1,"issueCount":0,"starsCount":4,"forksCount":3,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-17T19:11:56.509Z"}},{"type":"Public","name":"RankNormalize","owner":"genepattern","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-19T04:09:31.349Z"}},{"type":"Public","name":"docker-r-3-13","owner":"genepattern","isFork":false,"description":"R3.1.3 Docker Container for GP modules run in docker or on AWS Batch","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-04T21:12:52.106Z"}},{"type":"Public","name":"ConstellationMap","owner":"genepattern","isFork":false,"description":"A downstream visualization and analysis tool for gene set enrichment results with interactive web visualizer","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-04T20:51:34.356Z"}},{"type":"Public","name":"CummeRbund","owner":"genepattern","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-04T20:44:13.645Z"}},{"type":"Public","name":"VoomNormalize","owner":"genepattern","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-04T20:19:18.899Z"}},{"type":"Public","name":"ExpressionFileCreator","owner":"genepattern","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-03T20:28:59.845Z"}},{"type":"Public","name":"MethylationCNVAnalysis","owner":"genepattern","isFork":false,"description":"","allTopics":["methylation","copy-number-variation","genepattern-module","methylation-microarray-data","cnv-analysis","conumee"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-04T19:24:03.354Z"}},{"type":"Public","name":"NMFConsensus","owner":"genepattern","isFork":false,"description":"Non-negative Matrix Factorization (NMF) Consensus Clustering GenePattern module","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-07T19:06:27.194Z"}},{"type":"Public","name":"docker-amaretto","owner":"genepattern","isFork":false,"description":"Docker container and module wrapper for Amaretto from the Gavaert Lab at Stanford (http://med.stanford.edu/gevaertlab/software.html)","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-13T21:13:55.392Z"}},{"type":"Public","name":"Conos.VisualizeGeneExpression","owner":"genepattern","isFork":false,"description":"Visualize expression of genes of interest after Conos.Cluster has been ran.","allTopics":["single-cell","singlecell","genepattern-module"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-07-20T19:03:43.047Z"}},{"type":"Public","name":"SubMap","owner":"genepattern","isFork":false,"description":"Maps subclasses between two data sets","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":3,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-07-19T16:38:26.854Z"}},{"type":"Public","name":"ssGSEA.ROC","owner":"genepattern","isFork":true,"description":"Generate ROC curves and calculate the AUC from ssGSEA results and a binary phenotype classification.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-05-17T13:46:25.914Z"}},{"type":"Public","name":"Seurat.IntegrateData","owner":"genepattern","isFork":false,"description":"GenePattern module which implements the batch correction algorithm within Seurat.","allTopics":["data-integration","batch-correction","seurat","genepattern-module","seurat-objects"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"BSD 3-Clause \"New\" or \"Revised\" License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-03-24T18:29:20.357Z"}},{"type":"Public","name":"PreprocessVelocityTranscriptome","owner":"genepattern","isFork":true,"description":"Transcriptome preprocessing for RNA Velocity wrapper module for GenePattern. ","allTopics":["utilities","preprocess","single-cell","genepattern-module"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-02-25T21:50:02.475Z"}},{"type":"Public archive","name":"HAPSEG","owner":"genepattern","isFork":false,"description":"A probabilistic method to interpret bi-allelic marker data in cancer samples.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-12-20T21:21:24.318Z"}},{"type":"Public archive","name":"ABSOLUTE","owner":"genepattern","isFork":false,"description":"Contains gp-unit tests for ABSOLUTE modules","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":6,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-12-14T19:16:30.960Z"}},{"type":"Public","name":"ComparativeMarkerSelection","owner":"genepattern","isFork":false,"description":"Identify differentially expressed genes that can discriminate between distinct classes of samples.","allTopics":["differential-expression","genepattern-module","gene-list-selection"],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-10-04T19:38:36.410Z"}},{"type":"Public","name":"DiffDatasets","owner":"genepattern","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-09-10T21:38:59.013Z"}}],"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":"genepattern repositories"}