{"id":13593439,"url":"https://github.com/kharchenkolab/dropEst","last_synced_at":"2025-04-09T05:31:16.967Z","repository":{"id":37650500,"uuid":"97519271","full_name":"kharchenkolab/dropEst","owner":"kharchenkolab","description":"Pipeline for initial analysis of droplet-based single-cell RNA-seq data","archived":false,"fork":false,"pushed_at":"2022-06-22T02:15:17.000Z","size":49343,"stargazers_count":84,"open_issues_count":41,"forks_count":43,"subscribers_count":15,"default_branch":"master","last_synced_at":"2024-05-22T18:12:52.462Z","etag":null,"topics":["pipeline","preprocessing","scrna-seq","single-cell-rna-seq"],"latest_commit_sha":null,"homepage":null,"language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/kharchenkolab.png","metadata":{"files":{"readme":"README.rst","changelog":"CHANGELOG.rst","contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2017-07-17T20:28:48.000Z","updated_at":"2024-04-08T17:56:54.000Z","dependencies_parsed_at":"2022-09-07T22:00:19.618Z","dependency_job_id":null,"html_url":"https://github.com/kharchenkolab/dropEst","commit_stats":null,"previous_names":[],"tags_count":7,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kharchenkolab%2FdropEst","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kharchenkolab%2FdropEst/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kharchenkolab%2FdropEst/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kharchenkolab%2FdropEst/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kharchenkolab","download_url":"https://codeload.github.com/kharchenkolab/dropEst/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247986572,"owners_count":21028881,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["pipeline","preprocessing","scrna-seq","single-cell-rna-seq"],"created_at":"2024-08-01T16:01:20.317Z","updated_at":"2025-04-09T05:31:13.255Z","avatar_url":"https://github.com/kharchenkolab.png","language":"C++","funding_links":[],"categories":["Software packages"],"sub_categories":["Other applications"],"readme":"dropEst - Pipeline\n==================\n\nPipeline for estimating molecular count matrices for droplet-based\nsingle-cell RNA-seq measurements. If you use the pipeline in your\nresearch, please `cite \u003c#citation\u003e`__ the corresponding\n`paper \u003chttps://doi.org/10.1186/s13059-018-1449-6\u003e`__. To reproduce\nresults from the paper, please see `this\nrepository \u003chttps://github.com/VPetukhov/dropEstAnalysis\u003e`__.\n\nDocumentation\n-------------\n\nFor detailed explanations, please see the `documentation \u003chttps://dropest.readthedocs.io/en/latest/\u003e`__\n\nParticularly:\n\n- `Installation \u003chttps://dropest.readthedocs.io/en/latest/setup.html#installation\u003e`__\n- `Integration with Velocyto \u003chttps://dropest.readthedocs.io/en/latest/dropest.html#velocyto-integration\u003e`__\n\nIf you have problems with installation, please look at the `Troubleshooting \u003chttps://dropest.readthedocs.io/en/latest/setup.html#troubleshooting\u003e`__ page and open an `issue \u003chttps://github.com/hms-dbmi/dropEst/issues\u003e`__ if there is nothing.\n\nNews\n----\n\n[0.8.6] - 2019-08-01\n~~~~~~~~~~~~~~~~~~~~\n\n-  Added support for Drop-seq and CEL-Seq2\n\nSee `Changelog \u003chttps://github.com/hms-dbmi/dropEst/blob/develop/CHANGELOG.rst\u003e`__ for the full list.\n\nGeneral processing steps\n------------------------\n\n1. **dropTag**: extraction of cell barcodes and UMIs from the library.\n   Result: demultiplexed .fastq.gz files, which should be aligned to the\n   reference.\n2. **Alignment** of the demultiplexed files to reference genome. Result:\n   .bam files with the alignment.\n3. **dropEst**: building count matrix and estimation of some statistics,\n   necessary for quality control. Result: .rds file with the count\n   matrix and statistics. *Optionally: count matrix in MatrixMarket\n   format.*\n4. **dropReport** - Generating report on library quality.\n5.  `dropEstR \u003chttps://github.com/kharchenkolab/dropestr\u003e`__ - R pacakge for UMI count corrections and cell quality classification\n\n\nExamples\n--------\n\nComplete examples of the pipeline can be found at\n`EXAMPLES.md \u003cexamples/EXAMPLES.md\u003e`__.\n\n`Here \u003chttp://pklab.med.harvard.edu/viktor/dropest_paper/dropest_0.8.5.zip\u003e`__\nare results of processing of\n`neurons\\_900 \u003chttps://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/neurons_900\u003e`__\n10x dataset.\n\nSupported protocols\n-------------------\n\n- 10x\n- CEL-Seq2\n- Drop-seq\n- iCLIP\n- inDrop (v1-3)\n- Seq-Well\n- SPLiT-seq\n\nCitation\n--------\n\nIf you find this pipeline useful for your research, please consider citing the paper:\n\nPetukhov, V., Guo, J., Baryawno, N., Severe, N., Scadden, D. T.,\nSamsonova, M. G., \u0026 Kharchenko, P. V. (2018). dropEst: pipeline for\naccurate estimation of molecular counts in droplet-based single-cell\nRNA-seq experiments. Genome biology, 19(1), 78.\ndoi:10.1186/s13059-018-1449-6\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkharchenkolab%2FdropEst","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkharchenkolab%2FdropEst","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkharchenkolab%2FdropEst/lists"}