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perseus:start [2016/09/22 13:40]
art [Perseus]
perseus:start [2018/10/19 09:34] (current)
rudolph [Cite] Add link to PerseusNet manuscript
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-{{ :​logo128x128.png?​200|}} 
 ====== Perseus ====== ====== Perseus ======
 +The Perseus software platform supports biological and biomedical researchers in interpreting protein quantification,​ interaction and post-translational modification data. Perseus contains a comprehensive portfolio of statistical tools for high-dimensional omics data analysis covering normalization,​ pattern recognition,​ time-series analysis, cross-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 signatures. Central 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 |}}
  
-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 [[MaxQuant:start]]and thus completes ​the proteomics analysis pipelineThe software is implemented in a practical format consisting of a main core to which plugins are addedThis allows easy integration of an unlimited number of independent statistical tools, which can thus be combined in an analysisThe software already includes various statistical methods ​and illustrations,​ such as data transformation,​ normalization and imputation, unsupervised 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.+==== Learn ==== 
 +  * Hands-on tutorials and theoretical lectures are available on the [[https://​www.youtube.com/​channel/​UCKYzYTm1cnmc0CFAMhxDO8w|MaxQuant ​youtube channel]]. 
 +  * Participate in our annual [[http://​summerschool.maxquant.de|MaxQuant summer school]] to gain even deeper insights into MaxQuant ​and Perseus. 
 +  * Read the protocol-style [[https://​link.springer.com/​protocol/​10.1007/​978-1-4939-7493-1_7|book chapter]] on Perseus. 
 +  * Join the discussion around Perseus ​and data analysis on the [[https://​groups.google.com/​forum/#​!forum/​perseus-list|Perseus mailing list]] -- a great place to ask any question and get answers ​from the community.
  
-To run Perseus, you will need .NET framework 4.5. If you use Windows you should have Vista or newer. Like most Windows software, Perseus can also be run on a Mac. There is currently no support for linuxbut it is [[http://​www.drdobbs.com/​windows/​c-and-nets-sudden-ubiquity/​240169282|on the horizon]].+==== Download ==== 
 +Perseus is freely available to commercial and academic usersjust 
 +follow the [[perseus:common:​download_and_installation|download ​and installation guide]].
  
-**A note to internal users:** Scientists at the Max Planck Institute of Biochemistry have access to Perseus ​features that have not yet been released to the public. To view the documentation ​of these features, you will have to log in using the button in the upper right corner of this pageIf you do not yet have an account, you will need to register using the button next to the login button and then ask Art Carlson to add you to the internal group.+==== Cite ==== 
 +If you use Perseus in your project, please cite:\\ 
 +[[https://​www.nature.com/​articles/​nmeth.3901|The ​Perseus ​computational platform for comprehensive analysis ​of (prote)omics data]] //NatMethods 2016//.
  
-==== Documentation outline ==== +Network analysisco-expression ​and PluginInterop:\\ 
-This documentation is organized as a wikiso 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 wiki, but to make changes you will have to register ​and login using the button in the upper right. ​          +[[https://​www.biorxiv.org/​content/​early/​2018/​10/​18/​447268|A network module for the Perseus software for computational proteomics facilitates proteome interaction graph analysis]] //BioRxiv 2018//.
-  * [[perseus:common:​Download and installation|Download and installation]] +
-  ​* ​[[perseus:user:User Interface]] +
-  * [[perseus:​noedit:​activities|Activities]] +
-  * [[perseus:​user:​plugins:​start]] +
-  * [[perseus:​user:​Tutorials]] +
-  * [[perseus:​user:​use_cases:​start]] +
-  * [[perseus:​common:​Google groups]] +
-  * [[perseus:​common:​Bug reporting]] +
-<ifauth @internal> ​ * [[perseus:​common:​internal:​Glossary]] +
-  * [[perseus:​internal:​FAQ]]<​/ifauth>+
  
 +Find a predictive protein signature using SVMs:\\
 +[[https://​www.nature.com/​articles/​ncomms10259|Proteomic maps of breast cancer subtypes]] //Nat. Comm. 2016//.
  
 +Perform 1D or 2D annotation enrichment:​\\
 +[[https://​www.ncbi.nlm.nih.gov/​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://​mqsummerschool.biochem.mpg.de/​summerschool2015/​welcome.html|MaxQuant Summer School]]. Also watching some [[http://​www.youtube.com/​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:​common:​Contact?​wiki=perseus]]+
perseus/start.1474544404.txt.gz · Last modified: 2016/09/22 13:40 by art