Discover bhklab/PharmacoGx Open Source project by BHKLAB (@bhklab)

Transparent and reproducible medical image processing pipelines in Python.

med-imagetools

Boilerplate for PyTorch Lightning based medical-image segmentation pipeline for to enable automated segmentation of organs-at-risk (in head and neck cancer) by using Simple Open-Source 3D CNNS

ptl-oar-segmentation

R package providing various functions relevant for gene expression analysis with emphasis on breast cancer.

genefu

mRMRe

mRMRe is a package for Parallelized Minimum Redundancy, Maximum Relevance (mRMR) Ensemble Feature Selection

CREAM (Clustering of Functional Regions Analysis Method) is a new method for identification of clusters of functional regions (COREs) within chromosomes.

CREAM

PGx_Guidelines

Workshop for Machine Learning in pharmacogenomics

PharmacoGxML

survcomp

R package for performance assessment and comparison for survival analysis

Official repository of the 2020 UHN RADCURE challenge.

uhn-radcure-challenge

PymRMRe

This package contains a set of functions related to network inference combining genomic data and prior information extracted from biomedical literature and structured biological databases.The main function is able to generate networks using bayesian or regression-based inference methods; while the former is limited to < 100 of variables, the latter may infer network with hundreds of variables. Several statistics at the edge and node levels have been implemented (edge stability, predictive ability of each node, ...) in order to help the user to focus on high quality subnetworks. Ultimately, this package is used in the 'Predictive Networks' web application developed by the Dana-Farber Cancer Institute in collaboration with Entagen

predictionet

XEnograft Visualization & Analysis

Xeva

PredictIO

RNASeqDrug

Gene isoforms as expression-based biomarkers predictive of drug response in vitro

ToxicoGx

A statistical package, in R, used in cancer research to analyze toxicity of drugs on cancer gene expression across large-scale toxicogenomic datasets.

RadioGx

RadioGx and PharmacoGx: Integrated prediction tools for combining radiotherapy with systemic agents

MetaGx

Scripts to perform meta-analysis of cancer gene expression datasets

DNF

Drug Network Fusion: Data integration from multiple drug information layers

PharmacoDB-JS

Search across publicly available datasets to find instances where a drug or cell line of interest has been profiled.

A workshop on drug combination experiment support in CoreGx and PharmacoGx.

bioc2022workshop

bioc2020workshop

A workshop on using high throughput screening experiments in the realm of biomarker discovery.

Dockerfile

MetaGxBreast

ORCESTRA

ORCESTRA is a new web application that enables users to search, request and manage pharmacogenomic datasets (PSets).

An web application that allows users to explore gene signatures in immunotherapy studies of ICB-treated patients, and to obtain gene signature predictions using molecular data of their own studies of ICB-treated patients.

PredictIO-webapp

Inconsistency in large pharmacogenomic studies

cdrug

RLOBICO

R implementation of Logic Optimization for Binary Input to Continuous Output (LOBICO)

eacon_cnv_pipeline

TGGATES

consensusOV

Implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer.

CoreGx

Shared code for both PharmacoGx and RadioGx

EpiStromaImmune

ConsensusPGxPaper

HTML

CrosstalkNet

A web resource to analyze bi-partite and non-bipartite biological networks.

Modified Concordance Index for pharmacological readout

wCI

cdrug2

Code for "Revisiting Inconsistency in Large Pharmacogenomic Studies"

FDA_MDACC

FDA study of inter‐laboratory and inter‐platform reproducibility of microarray‐based gene expression measurements

DRUGNET

TCRP_Reusability_Report

Metric Learning on L1K, and other datasets

metriclearning

snakemake-kubernetes-api

Flask API to be used as the new data processing layer of ORCESTRA.

The PharmacoDI Python package contains all the functions needed to make the PharmacoDB database tables from a collection of .csv for each PSet.

ISMB-2019

HTML

PharmacoDI

GraphComm

Radiomic Extraction and Analysis for DICOM Images (READII)

RadioGx-analysis

AnnotationExamples

readii

PDATK

NCI-PDMR-Data

MATLAB

OvcSubtypes

MetaGxOvarian

QUANNOTATE

Analysis pipeline implementing the response to the rebuttal letters in Nature

cdrug-rebuttals

DrugVIPER

PDACsurv

Meta-analysis of prognostic models for PDAC

PDAC-Subtyping-DrugResponse

longArray

longArray Example

Snakemake

Perl

GeneFusionDrug

Robust detection of gene fusions and their association with drug response in cancer cell lines

AnnotationGx

An R package to query various bio/chem-informatics databases APIs to construct annotation files.

ALTAR

R Interface for PharmacoDB

DNA11161

RPharmacoDB

affymetrix_cnv_pipeline

Snakemake pipeline for calling CNAs from Affymetrix (now Thermofisher) Cytoscan and Oncoscan arrays

MetaGxData

Analysis pipeline for the MetaGxData package compedium (version 2.3)

Gene_Expression_Bimodality

illuminaEPICmethylation

Snakemake pipeline for analyzing Illumina EPIC methylation array data

wCI-libraries

Shared C code libraries for computing the wCI

SYNERGxDB

SYNERGxDB is a comprehensive database to explore synergistic drug combinations for biomarker discovery.

R code which enchances the PharmacoDI Python package.

rPharmacoDI

PharmacoDI_snakemake_pipeline

A Snakemake pipeline to automate the scripts for creating all PharmacoDB database tables and allow easy deployment on a range of platforms.