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ComputationalProteomicsUnit · Jul 18, 2018 · 97b24b5 · 97b24b5
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+.Rhistory
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@@ -1,8 +1,6 @@
 # biotinIDR : Contains code and input files for Biotin IDR study 
-### Authors :	David Paul Minde and Manasa Ramakrishna
-
-#### Main code  : R and Python code for analysing data
 
+### Main code  : R and Python code for analysing data
 Note: Before you run this code, you will need to download the following scripts
 1. R installed on your computer  
 2. Python installed on your computer 
@@ -23,7 +21,7 @@ d2p2.py	|	Tom's code to use the d2p2 API to use 9 different callers to identify
 protinfo.py	|	 Tom's code to query uniprot/swissprot database on Ensembl	|	Python  
 
 
-#### Input : Folder containing all input files needed for code to run
+### Input : Folder containing all input files needed for code to run
 
 File| Contents   
 ----------|------------- 
@@ -38,6 +36,7 @@ HEK293-with-IDR-VSL2b-and-PTMs.rds	|	HEK293 peoteins from Geiger et al with PTMs
 PTMs-by-gene-from-Phosphositeplus.rds	|	PTM data from PhosphositePlus summarised by gene and for phosphorylation, ubiquitination, sumoylation, acetylation  
 go-pro-kegg.rda	|	An object that contains all GO, Interpro and KEGG annotations for proteins in each of the 4 studies  
 
+
 #### RDS files can be read using the command readRDS as shown below
 ```
 readRDS("Input/Biotin-PTM-IDR-data-for-all-studies-and-callers.rds")
@@ -48,7 +47,7 @@ readRDS("Input/Biotin-PTM-IDR-data-for-all-studies-and-callers.rds")
 load("Input/go-pro-kegg.rda")
 ```
 
-#### Output : A description of all files generated by running nods_final.Rmd.  
+### Output : A description of all files generated by running nods_final.Rmd.  
 
 Date_Output : Date-tagged output folder This folder should contain the following files
 Date = Date of the analysis in format yyyy-mm-dd ; Time = Time of analysis in format hh:mm:ss  
@@ -82,6 +81,7 @@ Date_Time_Effect-size-for-pairwise-comparison-of-IDR-classes-and-parameters-VSL2
 Date_Time_VSL2b_Pairwise-t-test-pvals.txt
 Date_Time_VSL2b_Tukey-HSD-ci-pvals.txt
 
+### Figures : Folder containing all main and supplementary Figures from the paper
 
 #### SupplTables.xlsx :  
 Supplementary tables referred to in the manuscript. Contain data that can be queried/used. Contains 5 datasheets and an "Index" sheet describing each of the data sheets.