praveenmunagapati / drug_sensitivity_ml

Machine Learning predictions of cancer cell sensitivity to different drugs using data from CCLE (Cancer Cell Line Encyclopedia).

drug_sensitivity_ML

This repository contains scripts pertaining to apply PSL (Probablistic Soft Logic) to cancer cell sensitivity to drugs using data from CCLE (Cancer Cell Line Encyclopedia) and Project Achilles.
To read more about PSL: https://psl.umiacs.umd.edu
To read more about CCLE: https://portals.broadinstitute.org/ccle/home
To read more about Achilles: https://portals.broadinstitute.org/achilles

project structure (updated 10-9-2016)

psl/    maven project and java/groovy/python codes for PSL applied to drug sensitity data
intelliJ-psl/    use intelliJ IDE to run psl groovy project files
profiling/  python or jupyter notebook script aiming at understanding/profiling of data
evaluation/ python folder to calculate accuracies of psl result
generate_data.py    python code to convert raw data into psl input format
configure_intelliJ_for_psl.md   instruction to configure psl MAVEN project with groovy support in IntelliJ IDEA 

List of data files (updated 10-06-2016)

----------------------------- RAW Data ------------------------------------------------------
## Downloaded from project Achilles https://portals.broadinstitute.org/achilles
Achilles_QC_v2.4.3.rnai.Gs.gct
Achilles_v2.4_SampleInfo_small.txt
Achilles_v3.3.8.Gs.gct
Achilles_v3.3.8_SampleInfo.txt

## Downloaded from CCLE https://portals.broadinstitute.org/ccle/home
CCLE_Expression_Entrez_2012-09-29.gct
CCLE_MUT_CNA_AMP_DEL_binary_Revealer.gct
CCLE_NP24.2009_Drug_data_2015.02.24.csv
CCLE_NP24.2009_profiling_2012.02.20.csv
CCLE_Oncomap3_2012-04-09.maf
CCLE_copynumber_byGene_2013-12-03.txt
CCLE_hybrid_capture1650_hg19_NoCommonSNPs_NoNeutralVariants_CDS_2012.05.07.maf
CCLE_sample_info_file_2012-10-18.txt 

## drug target data compiled by Verina and Kiley
combined_annotations_CCLEmapped.tab

------------------------- generated data ----------------------------------------------------
## percentile of raw files (each value is converted to a percentile respective to its column)
Achilles_QC_v2.4.3.rnai.Gs.percentgct
CCLE_Expression_Entrez_2012-09-29.percentgct
CCLE_NP24.2009_Drug_data_2015.02.24.ActAreaPercentcsv

Using locally installed maven dependencies example:

<dependency>
    <groupId>edu.umd.cs</groupId>
    <artifactId>psl-groovy</artifactId>
    <version>2.0-SNAPSHOT</version>
</dependency>

Path to maven locally installed .jar file: ~/.m2/repository/edu/umd/cs/psl-groovy/2.0-SNAPSHOT/