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perseus:start [2016/09/22 13:24]
art [Perseus]
perseus:start [2018/07/18 16:13]
rudolph [Learn]
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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 [[MaxQuant:start]], and thus completes the proteomics analysis pipeline. The software is implemented in a 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 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 more. Additionally,​ it is possible to combine data from all omics sources for systems-wide analyses.+{{ :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 [[http://www.drdobbs.com/windows/c-and-nets-sudden-ubiquity/​240169282|on the horizon]].+==== 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.
  
-**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 featuresyou will have to log in using the button in the upper right corner of this page. If you have problems, contact Art Carlson.+==== 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:\\ [[https://​www.nature.com/​articles/​nmeth.3901|"The Perseus computational platform for comprehensive analysis of (prote)omics data"]] //Nat. Methods 2016//.
-  * [[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>+
  
 +=== Additional publications ===
 +Please consider citing the following articles if applicable.
 +  * 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//.
  
 +==== Report a bug ====
  
-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. +See our [[perseus:common:report_bug|'​Report a bug']] page.
- +
-**__Comment:​__** In the newest Perseus version we changed the terminology of expression columns to main columns. The functionality of these columns is equivalent. +
- +
-//Footnote on [[perseus:​pronunciation]].//​ +
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-[[perseus:​common:​Contact?​wiki=perseus]]+
perseus/start.txt · Last modified: 2018/10/19 09:34 by rudolph