{"id":27351943,"url":"https://github.com/genometric/mspc","last_synced_at":"2025-04-12T20:54:12.096Z","repository":{"id":23139307,"uuid":"98246154","full_name":"Genometric/MSPC","owner":"Genometric","description":"Using combined evidence from replicates to evaluate ChIP-seq 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align=\"center\"\u003e\n  \u003ca href=\"https://genometric.github.io/MSPC/\"\u003e\n    \u003cimg src=\"https://raw.githubusercontent.com/Genometric/MSPC/dev/website/static/logo/logo_w_txt_banner.svg?raw=true\" alt=\"MSPC\" width=\"300\" /\u003e\n  \u003c/a\u003e\n\u003c/p\u003e\n\n\n\u003cp align=\"center\"\u003e\n    \u003ca href=\"https://www.nuget.org/packages/Genometric.MSPC.Core\"\u003e\n        \u003cimg src=\"https://img.shields.io/nuget/v/Genometric.MSPC.Core?style=flat\u0026color=%2390c04f\u0026link=https%3A%2F%2Fwww.nuget.org%2Fpackages%2FGenometric.MSPC.Core%2F\"\u003e\n    \u003c/a\u003e\n    \u003ca href=\"https://sonarcloud.io/project/overview?id=genometric_mspc\"\u003e\n        \u003cimg src=\"https://sonarcloud.io/api/project_badges/measure?project=genometric_mspc\u0026metric=alert_status\"\u003e\n    \u003c/a\u003e\n    \u003ca href=\"https://codecov.io/gh/Genometric/MSPC\"\u003e\n    \u003cimg src=\"https://codecov.io/gh/Genometric/MSPC/branch/master/graph/badge.svg?token=TRSk39hCh3\"/\u003e\n    \u003c/a\u003e\n    \u003ca href=\"https://sonarcloud.io/summary/new_code?id=genometric_mspc\"\u003e\n        \u003cimg src=\"https://sonarcloud.io/api/project_badges/measure?project=genometric_mspc\u0026metric=ncloc\"\u003e\n    \u003c/a\u003e\n    \u003ca href=\"https://sonarcloud.io/summary/new_code?id=genometric_mspc\"\u003e\n        \u003cimg src=\"https://sonarcloud.io/api/project_badges/measure?project=genometric_mspc\u0026metric=sqale_rating\"\u003e\n    \u003c/a\u003e\n    \u003ca href=\"https://sonarcloud.io/summary/new_code?id=genometric_mspc\"\u003e\n        \u003cimg src=\"https://sonarcloud.io/api/project_badges/measure?project=genometric_mspc\u0026metric=reliability_rating\"\u003e\n    \u003c/a\u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n  \u003ca href=\"https://genometric.github.io/MSPC/docs/quick_start\"\u003eQuick Start\u003c/a\u003e |\n  \u003ca href=\"https://genometric.github.io/MSPC/\"\u003eDocumentation\u003c/a\u003e |\n  \u003ca href=\"https://github.com/Genometric/MSPC/releases\"\u003eDownload\u003c/a\u003e |\n  \u003ca href=\"https://genometric.github.io/MSPC/publications\"\u003ePublication\u003c/a\u003e\n\u003c/p\u003e\n\n## About\n\nThe analysis of ChIP-seq samples outputs a number of enriched regions, \neach indicating a protein-DNA interaction or a specific chromatin \nmodification. Enriched regions (commonly known as \"peaks\") are called \nwhen the read distribution is significantly different from the background \nand its corresponding significance measure (p-value) is below a \nuser-defined threshold.\n\nWhen replicate samples are analysed, overlapping enriched regions are \nexpected. This repeated evidence can therefore be used to locally lower \nthe minimum significance required to accept a peak. Here, we propose a \nmethod for joint analysis of weak peaks.\n\nGiven a set of peaks from (biological or technical) replicates, the method \ncombines the p-values of overlapping enriched regions: users can choose a \nthreshold on the combined significance of overlapping peaks and set a \nminimum number of replicates where the overlapping peaks should be present. \nThe method allows the \"rescue\" of weak peaks occuring in more than one \nreplicate and outputs a new set of enriched regions for each replicate. \n\nIn general, the method groups enriched regions as \n[_background_](https://genometric.github.io/MSPC/docs/method/sets#background), \n[_weak_](https://genometric.github.io/MSPC/docs/method/sets#weak),\nor [_stringent_](https://genometric.github.io/MSPC/docs/method/sets#stringent)\nbased on user-defined \n[weak](https://genometric.github.io/MSPC/docs/cli/args#weak-threshold) \nand [stringency thresholds](https://genometric.github.io/MSPC/docs/cli/args#stringency-threshold). \nThe method then [_confirms_](https://genometric.github.io/MSPC/docs/method/sets#confirmed)\nor [_discards_](https://genometric.github.io/MSPC/docs/method/sets#discarded)\nthe _weak_ and _stringent_ enriched regions if their combined stringency is at least as significant \nas a [user-defined threshold](https://genometric.github.io/MSPC/docs/cli/args#gamma). \nThe method then performs a multiple testing correction on \n_confirmed_ enriched regions at \n[a user-defined false-discovery rate](https://genometric.github.io/MSPC/docs/cli/args#alpha), \nidentifying \n[true-positive](https://genometric.github.io/MSPC/docs/method/sets#truepositive) and \n[false-positive](https://genometric.github.io/MSPC/docs/method/sets#falsepositive)\nregions. See the following figure as an example, and you may refer to \n[MSPC publications](https://genometric.github.io/MSPC/publications),\n[slides on slideshare](http://www.slideshare.net/jalilivahid/mspc-50694133),\nor [documentation](https://genometric.github.io/MSPC/docs/method/about) \npage for more details.\n\n\u003cp align=\"center\"\u003e\n    \u003ca href=\"https://genometric.github.io/MSPC/docs/method/sets\"\u003e\n        \u003cimg src=\"https://raw.githubusercontent.com/Genometric/MSPC/dev/website/static/img/sets.svg\"\u003e\n    \u003c/a\u003e\n\u003c/p\u003e\n\n\n\u003cbr/\u003e\n\n## Download and Run\n\n- #### [__Quick Start__: _download, install, and run a demo use-case_](https://genometric.github.io/MSPC/docs/quick_start);\n- #### [__Install__: _details on different installation options_](https://genometric.github.io/MSPC/docs/installation);\n- #### [__Bioconductor R package__:](https://bioconductor.org/packages/release/bioc/html/rmspc.html) [Bioconductor user guide with examples on installing and using it in R](https://bioconductor.org/packages/release/bioc/vignettes/rmspc/inst/doc/rmpsc.html). \n\nMSPC is distributed as a cross-platform console application, a .NET library, \nand a Bioconductor R package. 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