Projects in Awesome Lists by bhklab
A curated list of projects in awesome lists by bhklab .
https://github.com/bhklab/pharmacogx
R package to analyze large-scale pharmacogenomic datasets.
datasets pharmacogenomic pharmacogx
Last synced: 06 Apr 2025
https://github.com/bhklab/pharmacodb
Search across publicly available datasets to find instances where a drug or cell line of interest has been profiled.
cell-lines datasets drug-dose-response-curves drug-targets drugs experiments tissues
Last synced: 13 Apr 2025
https://github.com/bhklab/med-imagetools
Transparent and reproducible medical image processing pipelines in Python.
deep-learning dicom machine-learning medical nifti nrrd python pytorch torch
Last synced: 06 Apr 2025
https://github.com/bhklab/genefu
R package providing various functions relevant for gene expression analysis with emphasis on breast cancer.
Last synced: 13 Apr 2025
https://github.com/bhklab/ptl-oar-segmentation
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
convolutional-neural-networks deep-learning medical-imaging monai open-source pytorch pytorch-lightning pytorchlightning segmentation
Last synced: 13 Apr 2025
https://github.com/bhklab/mrmre
mRMRe is a package for Parallelized Minimum Redundancy, Maximum Relevance (mRMR) Ensemble Feature Selection
Last synced: 13 Apr 2025
https://github.com/bhklab/uhn-radcure-challenge
Official repository of the 2020 UHN RADCURE challenge.
Last synced: 13 Apr 2025
https://github.com/bhklab/CREAM
CREAM (Clustering of Functional Regions Analysis Method) is a new method for identification of clusters of functional regions (COREs) within chromosomes.
biomedical-informatics clustering functional-prediction peak-detection
Last synced: 19 Apr 2025
https://github.com/bhklab/cream
CREAM (Clustering of Functional Regions Analysis Method) is a new method for identification of clusters of functional regions (COREs) within chromosomes.
biomedical-informatics clustering functional-prediction peak-detection
Last synced: 13 Apr 2025
https://github.com/bhklab/pharmacogxml
Workshop for Machine Learning in pharmacogenomics
Last synced: 13 Apr 2025
https://github.com/bhklab/survcomp
R package for performance assessment and comparison for survival analysis
differential-expression gene-expression regression survival visualization
Last synced: 13 Apr 2025
https://github.com/bhklab/predictionet
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
Last synced: 13 Apr 2025
https://github.com/bhklab/metagx
Scripts to perform meta-analysis of cancer gene expression datasets
Last synced: 13 Apr 2025
https://github.com/bhklab/rnaseqdrug
Gene isoforms as expression-based biomarkers predictive of drug response in vitro
Last synced: 13 Apr 2025
https://github.com/bhklab/toxicogx
A statistical package, in R, used in cancer research to analyze toxicity of drugs on cancer gene expression across large-scale toxicogenomic datasets.
Last synced: 13 Apr 2025
https://github.com/bhklab/pharmacodb-js
Search across publicly available datasets to find instances where a drug or cell line of interest has been profiled.
cell-lines compounds datasets drug-dose-response-curves drug-targets experiments tissue
Last synced: 13 Apr 2025
https://github.com/bhklab/radiogx
RadioGx and PharmacoGx: Integrated prediction tools for combining radiotherapy with systemic agents
Last synced: 13 Apr 2025
https://github.com/bhklab/orcestra
ORCESTRA is a new web application that enables users to search, request and manage pharmacogenomic datasets (PSets).
Last synced: 13 Apr 2025
https://github.com/bhklab/bioc2020workshop
A workshop on using high throughput screening experiments in the realm of biomarker discovery.
Last synced: 20 Feb 2025
https://github.com/bhklab/dnf
Drug Network Fusion: Data integration from multiple drug information layers
Last synced: 13 Apr 2025
https://github.com/bhklab/predictio-webapp
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.
Last synced: 13 Apr 2025
https://github.com/bhklab/metriclearning
Metric Learning on L1K, and other datasets
Last synced: 30 Dec 2024
https://github.com/bhklab/bioc2022workshop
A workshop on drug combination experiment support in CoreGx and PharmacoGx.
Last synced: 13 Apr 2025
https://github.com/bhklab/cdrug
Inconsistency in large pharmacogenomic studies
Last synced: 20 Feb 2025
https://github.com/bhklab/rlobico
R implementation of Logic Optimization for Binary Input to Continuous Output (LOBICO)
Last synced: 20 Feb 2025
https://github.com/bhklab/coregx
Shared code for both PharmacoGx and RadioGx
pharmacogx pharmacogx-backend radiogx toxicogx
Last synced: 13 Apr 2025
https://github.com/bhklab/crosstalknet
A web resource to analyze bi-partite and non-bipartite biological networks.
Last synced: 13 Apr 2025
https://github.com/bhklab/snakemake-kubernetes-api
Flask API to be used as the new data processing layer of ORCESTRA.
Last synced: 13 Apr 2025
https://github.com/bhklab/metagxdata
Analysis pipeline for the MetaGxData package compedium (version 2.3)
Last synced: 13 Apr 2025
https://github.com/bhklab/wci
Modified Concordance Index for pharmacological readout
Last synced: 20 Feb 2025
https://github.com/bhklab/cdrug2
Code for "Revisiting Inconsistency in Large Pharmacogenomic Studies"
analysis pipeline reproducibility
Last synced: 20 Feb 2025
https://github.com/bhklab/pharmacodi
The PharmacoDI Python package contains all the functions needed to make the PharmacoDB database tables from a collection of .csv for each PSet.
Last synced: 20 Feb 2025
https://github.com/bhklab/fda_mdacc
FDA study of inter‐laboratory and inter‐platform reproducibility of microarray‐based gene expression measurements
Last synced: 20 Feb 2025
https://github.com/bhklab/consensusov
Implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer.
cancer-data cancer-genomics cancer-research expression-database ovarian-cancer
Last synced: 20 Feb 2025
https://github.com/bhklab/pdacsurv
Meta-analysis of prognostic models for PDAC
Last synced: 20 Feb 2025
https://github.com/bhklab/rpharmacodi
R code which enchances the PharmacoDI Python package.
Last synced: 20 Feb 2025
https://github.com/bhklab/synergxdb
SYNERGxDB is a comprehensive database to explore synergistic drug combinations for biomarker discovery.
Last synced: 13 Apr 2025
https://github.com/bhklab/annotationgx
An R package to query various bio/chem-informatics databases APIs to construct annotation files.
Last synced: 05 Mar 2025
https://github.com/bhklab/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.
Last synced: 20 Feb 2025
https://github.com/bhklab/analyze_readii_outputs
Code for analyzing outputs from the READII package or the readii-orcestra pipeline.
Last synced: 20 Feb 2025
https://github.com/bhklab/cdrug-rebuttals
Analysis pipeline implementing the response to the rebuttal letters in Nature
Last synced: 20 Feb 2025
https://github.com/bhklab/med-imagenet
Med-ImageNet processing scripts via Med-ImageTools AutoPipeline
Last synced: 20 Feb 2025
https://github.com/bhklab/xevadb
XevaDB is a database for PDX pharmacogenomic data.
Last synced: 20 Feb 2025
https://github.com/bhklab/icb_data_exploration_and_analysis
A repository for sample code used to explore and analyze ICB data objects. Code is in both R and Python
Last synced: 20 Feb 2025
https://github.com/bhklab/readii
Radiomic Extraction and Analysis for DICOM Images (READII)
Last synced: 05 Mar 2025
https://github.com/bhklab/affymetrix_cnv_pipeline
Snakemake pipeline for calling CNAs from Affymetrix (now Thermofisher) Cytoscan and Oncoscan arrays
Last synced: 20 Feb 2025
https://github.com/bhklab/illuminaepicmethylation
Snakemake pipeline for analyzing Illumina EPIC methylation array data
Last synced: 20 Feb 2025
https://github.com/bhklab/wci-libraries
Shared C code libraries for computing the wCI
Last synced: 20 Feb 2025
https://github.com/bhklab/genefusiondrug
Robust detection of gene fusions and their association with drug response in cancer cell lines
Last synced: 20 Feb 2025
https://github.com/bhklab/cfi402257
Delay of mitotic progression caused by impairment of the anaphase-promoting complex confers resistance to TTK inhibitors in triple-negative breast cancer
Last synced: 20 Feb 2025
https://github.com/bhklab/clinsets
R Data Package for clinical multimodal data
Last synced: 20 Feb 2025
https://github.com/bhklab/rasdependencyscore
Assessment of KRAS-dependency scores for predictive models in pancreatic ductal adenocarcinoma
Last synced: 20 Feb 2025
https://github.com/bhklab/azure-aks-snakemake
Managed Azure Kubernetes Service (AKS) cluster for deploying Snakemake jobs with dynamic resource allocation and scaling.
Last synced: 20 Feb 2025
https://github.com/bhklab/drugnetworkfusion
Web resource for inferring new hypotheses about the mode of action of chemical compounds prior to clinical use
Last synced: 20 Feb 2025
https://github.com/bhklab/xevadi
The XevaDI is a python package that transforms the CSV files from the Xeva set to create the database table for XevaDB.
Last synced: 20 Feb 2025
https://github.com/bhklab/zero_interaction_potency-reproduction
Repository reproducing the original ZIP paper: Yadav, B., et al . (2015). Searching for Drug Synergy in Complex Dose–Response Landscapes Using an Interaction Potency Model. DOI: https://doi.org/10.1016/j.csbj.2015.09.001
Last synced: 20 Feb 2025