A python implementation of the Statistical Coupling Analysis (SCA)
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Inputs
Outputs Initial commit of the pySCA toolbox Jan 30, 2016
figs Initial commit of the pySCA toolbox Jan 30, 2016
html_docs modified install instructions to fix shebang line May 2, 2016
.DS_Store Initial commit of the pySCA toolbox Jan 30, 2016
.gitignore Adding a .gitignore file Jan 31, 2016
LICENSE Initial commit of the pySCA toolbox Jan 30, 2016
README Initial commit of the pySCA toolbox Jan 30, 2016
SCA_DHFR.ipynb
SCA_G.ipynb Initial commit of the pySCA toolbox Jan 30, 2016
SCA_S1A.ipynb Initial commit of the pySCA toolbox Jan 30, 2016
SCA_betalactamase.ipynb Initial commit of the pySCA toolbox Jan 30, 2016
alnFilterSeqSize.py Initial commit of the pySCA toolbox Jan 30, 2016
alnParseGI.py
alnReplaceHeaders.py Initial commit of the pySCA toolbox Jan 30, 2016
annotate_MSA.py
runAllNBCalcs.sh Initial commit of the pySCA toolbox Jan 30, 2016
scaCore.py Initial commit of the pySCA toolbox Jan 30, 2016
scaProcessMSA.py Merge branch 'master' of https://github.com/reynoldsk/pySCA Apr 27, 2018
scaSectorID.py Initial commit of the pySCA toolbox Jan 30, 2016
scaTools.py Edited scaProcessMSA and scaTools to fix a few small bugs: Apr 27, 2018

README

#############################################################
# README file for pySCA
#
# 03.2015 
#
# Copyright (C) 2015 Olivier Rivoire, Rama Ranganathan, Kimberly
# Reynolds
# This program is free software distributed under the BSD 3-clause
# license, please see the file LICENSE for details.
#############################################################

The current version of the Statistical Coupling Analysis (SCA)
analysis is implemented in python. This directory contains the
necessary code for running the SCA calculations, as well examples/tutorials for
the dihydrofolate reductase (DHFR) enzyme family, the S1A serine
proteases, the small G-protein family and the Beta-lactamase enzyme
family. The tutorials are distributed as iPython notebooks; for
details please see: http://ipython.org/notebook.html

#############################################################

For installation instructions, and an introduction to using the
toolbox, please see:

https://github.com/reynoldsk/pySCA

or open the html files included with the pySCA distribution in a browser:

html_docs/index.html

#############################################################

Contents

   Inputs/		  :  Directory containing input files (including those
   		   	     needed for the tutorials)
  
   Outputs/   	   	  :  Directory for output files (empty at install)
  
   html_docs/             :  Directory containing html documentation

   annotate_MSA.py	  :  Python script that annotates alignments
   			     with phylogenetic/taxonomic information   

   scaProcessMSA.py	  :  Python script that conducts some initial
   			     processing of the sequence alignment
  
   scaCore.py             :  Python script that runs the core SCA calculations
  
   scaSectorID.py         :  Python script that defines sectors given the
   			     results of the calculations in scaCore
  
   scaTools.py		  :  The SCA toolbox - contains all functions
   			     needed for the SCA calculations
  
   SCA_DHFR.ipynb	  :  Python notebook example for DHFR
   
   SCA_G.ipynb		  :  Python notebook example for the small G proteins
   
   SCA_betalactamase.ipynb:  Python notebook example for the beta-lactamases

   SCA_S1A.ipynb	  :  Python notebook example for the S1A
                             serine protease
#############################################################