diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..dc528e5 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +.Rhistory diff --git a/Figures/Figure1.png b/Figures/Figure1.png new file mode 100644 index 0000000..c469386 Binary files /dev/null and b/Figures/Figure1.png differ diff --git a/Figures/Figure2.png b/Figures/Figure2.png new file mode 100644 index 0000000..ebad887 Binary files /dev/null and b/Figures/Figure2.png differ diff --git a/Figures/Figure3.png b/Figures/Figure3.png new file mode 100644 index 0000000..7e86d8e Binary files /dev/null and b/Figures/Figure3.png differ diff --git a/Figures/Figure4.png b/Figures/Figure4.png new file mode 100644 index 0000000..1eced6d Binary files /dev/null and b/Figures/Figure4.png differ diff --git a/Figures/Figure5.png b/Figures/Figure5.png new file mode 100644 index 0000000..0b65493 Binary files /dev/null and b/Figures/Figure5.png differ diff --git a/Figures/Figure6.png b/Figures/Figure6.png new file mode 100644 index 0000000..cd3b81b Binary files /dev/null and b/Figures/Figure6.png differ diff --git a/Figures/FigureS1.png b/Figures/FigureS1.png new file mode 100644 index 0000000..e8e944e Binary files /dev/null and b/Figures/FigureS1.png differ diff --git a/Figures/FigureS1C.png b/Figures/FigureS1C.png new file mode 100644 index 0000000..a0eeebe Binary files /dev/null and b/Figures/FigureS1C.png differ diff --git a/Figures/FigureS2.png b/Figures/FigureS2.png new file mode 100644 index 0000000..b31bace Binary files /dev/null and b/Figures/FigureS2.png differ diff --git a/Figures/FigureS3.png b/Figures/FigureS3.png new file mode 100644 index 0000000..05baabe Binary files /dev/null and b/Figures/FigureS3.png differ diff --git a/README.md b/README.md index ebb8ec1..9f5e53b 100644 --- a/README.md +++ b/README.md @@ -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.