Geena
Build June 18, 2019.
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This system is under active development,
You are welcome to send us your comments.
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Welcome to GeenaR, a tool for MALDI/ToF MS spectra analysis.

Using GeenaR should be straightforward.
Nevertheless, should you have any problem, see the help page and the page on information on format
See also the help page on how to run the test on the example dataset.

NB! Move your mouse over the icon for a contextual help.
Fields marked with a * are mandatory!

YOU MUST UPLOAD YOUR SPECTRA BEFORE RUNNING THE ANALYSIS. GO TO THE UPLOAD PAGE NOW IF YOU DID NOT DO IT YET.

 Job information
*Job name:
*Data set name:
*Email:
Country:
 Input data

*Target file:

Trimming: From: m/z
  To: m/z
Quality control:           Reporting: With code:
Attributes file:
  
 Steps, methods and parameters
Step (select to execute)
Select/unselect all steps
Method
Parameters
 Pre-processing of spectra
Variance stabilization SQRT LOG LOG2 LOG10  
Smoothing Savitsky-Golay Moving average Half window size:
Baseline removal SNIP TopHat Convex-Hull Median Number of iterations:    Half window size:
Normalization TIC PQN Median  
Averaging Mean Median Sum  
Alignment Noise estimation: MAD Super Smoother Half window size:   SNR:
  Phase correction: Lowess Linear Quadratic Cubic Tolerance:
 Peak identification, extraction and selection
Detection Binning: Strict Relaxed  
  Selection Coverage:
 Clustering and visualization
Clustering Link function: Average Complete Ward Median  
  K estimation: Gap Statistic Silhouette Manually given K value:
Heatmap Clustering: None Samples Signals Both  
Principal Component Analysis (PCA)    
  


For information, get in touch with:
Paolo Romano, Bioinformatics, IRCCS Ospedale Policlinico San Martino,
Email to Paolo.Romano@HSanMartino.it