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perseus:start [2015/11/23 11:31]
art [Documentation outline]
perseus:start [2018/10/19 09:34]
rudolph [Cite] Add link to PerseusNet manuscript
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-{{ :​logo128x128.png?​200|}} 
 ====== Perseus ====== ====== Perseus ======
-Perseus ​is software ​package for shotgun proteomics data analyses, which helps to extract biologically meaningful information from processed raw files. It performs bioinformatic analyses of the output of [[http://​​maxquant_doku/​doku.php?​id=start&#​maxquant|MaxQuant]], and thus completes the proteomics analysis pipelineThe software is implemented in practical format consisting of a main core to which plugins are added. This allows easy integration of an unlimited number ​of independent ​statistical tools, which can thus be combined in an analysis. The software already includes various statistical methods and illustrationssuch as data transformationnormalization and imputationunsupervised ​and supervised ​learning ​methods, correlation profiling, enrichment tests, motif identification,​ volcano plots, scatter plots, and many many moreAdditionally,​ it is possible to combine data from all omics sources for systems-wide analyses.+The Perseus software ​platform supports biological and biomedical researchers in interpreting protein quantificationinteraction ​and post-translational modification dataPerseus contains ​comprehensive portfolio ​of statistical tools for high-dimensional omics data analysis ​covering normalizationpattern recognitiontime-series analysiscross-omics comparisons ​and multiple-hypothesis testing. A machine ​learning ​module supports the classification and validation of patient groups for diagnosis and prognosis, and it also detects predictive protein signaturesCentral to Perseus ​is a user-friendly, interactive workflow environment that provides complete documentation of computational methods used in a publication. 
 +{{ :​perseus:​perseus_figure1.jpg?​nolink&​600 |}}
-To run Perseus, you will need .NET framework 4.5If you use Windows you should have Vista or newerLike most Windows software, ​Perseus ​can also be run on a MacThere is currently no support for linux, but it is [[​240169282|on the horizon]].+==== Learn ==== 
 +  * Hands-on tutorials and theoretical lectures are available on the [[https://​​channel/​UCKYzYTm1cnmc0CFAMhxDO8w|MaxQuant youtube channel]]. 
 +  * Participate in our annual [[http://​|MaxQuant summer school]] to gain even deeper insights into MaxQuant and Perseus. 
 +  * Read the protocol-style ​[[|book chapter]] ​on Perseus. 
 +  * Join the discussion around Perseus and data analysis on the [[https://​​forum/#​!forum/​perseus-list|Perseus mailing list]] -- a great place to ask any question and get answers from the community.
-\\+==== Download ==== 
 +Perseus is freely available to commercial and academic users, just 
 +follow the [[perseus:​common:​download_and_installation|download and installation guide]].
-==== Documentation outline ​==== +==== Cite ==== 
-This documentation is organized as a wiki, so if you find anything that is wrong or hard to understand, ​in most cases you can fix it yourself. The wiki can be browsed by using the links below or by searching with the box in the upper right. Anyone is allowed to read the wikibut to make changes you will have to register and login using the button in the upper right. ​         ​ +If you use Perseus ​in your projectplease cite:\\ 
-  ​* ​[[perseus:common:​Download and installation|Download and installation]] +[[https://​​articles/​nmeth.3901|The Perseus computational platform for comprehensive analysis of (prote)omics data]] //Nat. Methods 2016//.
-  * [[perseus:​user:​User Interface]] +
-  * [[perseus:​noedit:​activities]] +
-  * [[perseus:​user:​Plugins]] +
-  * [[perseus:​user:​Tutorials]] +
-  * [[perseus:​user:​Use cases]] +
-  * [[perseus:​common:​Glossary]] +
-  * [[perseus:​common:​Google groups]] +
-  * [[perseus:​common:​Bug reporting]]+
-<ifauth @internal> ​ * [[perseus:user:FAQ]]</ifauth>+Network analysis, co-expression and PluginInterop:​\\ 
 +[[https://​​content/​early/​2018/​10/​18/​447268|A network module for the Perseus software for computational proteomics facilitates proteome interaction graph analysis]] //BioRxiv 2018//.
 +Find a predictive protein signature using SVMs:\\
 +[[https://​​articles/​ncomms10259|Proteomic maps of breast cancer subtypes]] //Nat. Comm. 2016//.
 +Perform 1D or 2D annotation enrichment:​\\
 +[[https://​​pmc/​articles/​PMC3489530/​|1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data]] //BMC Bioinformatics 2012//.
-For additional training, consider attending the annual [[http://​​summerschool2015/​welcome.html|MaxQuant Summer School]]. Also watching some [[http://​​channel/​UCKYzYTm1cnmc0CFAMhxDO8w|MaxQuant videos]] provides more insight.+==== Report a bug ====
-**__Comment:​__** In the newest Perseus version we changed the terminology of expression columns to main columns. The functionality of these columns is equivalent. +See our [[perseus:​common:​report_bug|'​Report a bug']] page.
- +
-//Footnote on [[perseus:​pronunciation]].//​ +
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perseus/start.txt · Last modified: 2018/10/19 09:34 by rudolph