Projects in Awesome Lists by bhklab
A curated list of projects in awesome lists by bhklab .
https://github.com/bhklab/quantitative-review
Quantitative review of methods for analyzing multiple regions of interest (ROIs) in the context of engineered radiomics.
Last synced: 20 Feb 2025
https://github.com/bhklab/toxicosetpipeline
Contains the code necessary to build all ToxicoSet objects from raw data.
Last synced: 20 Feb 2025
https://github.com/bhklab/signaturesets
Compendium of published molecular signatures
Last synced: 20 Feb 2025
https://github.com/bhklab/toxicodb-web
ToxicoDB is a database of curated toxicogenomics datasets that provides convenient data summary and visualization to mine these complex data. Users can find drug and gene annotations, visualize differential gene expression and enriched pathways within datasets for drug of interest.
d3js drug nodejs plotlyjs reactjs toxicogenomics
Last synced: 20 Feb 2025
https://github.com/bhklab/statinemt
Project to regenerate the pharmacogenomics analysis in this paper: "Statin-induced cancer cell death can be mechanistically uncoupled from prenylation of RAS family proteins"
Last synced: 20 Feb 2025
https://github.com/bhklab/qanpcrt
Quality Assurance of Nasopharyngeal Cancer Radiation Therapy Targets (CTV's) using a novel web-based quality assurance application
cancer r radiation radiation-oncology radiation-therapy radiomics radiomics-analysis
Last synced: 20 Feb 2025
https://github.com/bhklab/dataingestion
A repo to hold the version controlled data injestion pipelines for various BHKLab web applications.
Last synced: 20 Feb 2025
https://github.com/bhklab/merida_snakemake_pipeline
Pipeline implementing the MERIDA logical modelling method using Snakemake to dispatch hyperparmeter tuning on a Slurm based HPC cluster.
Last synced: 20 Feb 2025
https://github.com/bhklab/metabias
A repository to study the impact of violating the independence assumption in meta-analysis on biomarker discovery
Last synced: 20 Feb 2025
https://github.com/bhklab/fastci
A nlogn implementation of the Concordance Index
Last synced: 20 Feb 2025
https://github.com/bhklab/cytoscanhdvshaloplextargetseq
Analysis assessing how well a Haloplex Targeted Sequencing panel of ~800 genes recapitulates results from a larger Cytoscan HD whole genom SNP array.
Last synced: 20 Feb 2025
https://github.com/bhklab/cosinedistr
Simulations for 'On the Distribution of cosine similarity with application to biology.'
Last synced: 20 Feb 2025
https://github.com/bhklab/demo-githubprojectmanagement
A demo and some documentation for using GitHub as our project management tool.
Last synced: 20 Feb 2025
https://github.com/bhklab/azure-aks-snakemake-merida
Scripts to configure and run the MERIDA_snakemake_pipeline on Azure Kubernetes Service
Last synced: 20 Feb 2025
https://github.com/bhklab/orcestra2cbio
Script to download ICB data from ORCESTRA and creates files to upload to cBioPortal
Last synced: 20 Feb 2025
https://github.com/bhklab/netinfpriors
R code accompanying Olsen et al., Frontiers In Genetics, 2014
Last synced: 20 Feb 2025
https://github.com/bhklab/kulgap
KuLGap is a web application that allows users to calculate KuLGaP as well as several other measurements of response to anti-tumour therapy.
Last synced: 20 Feb 2025
https://github.com/bhklab/leukemia-heterogeneity-analysis
Heterogeneity in leukemia cells that escape drug-induced senescence-like state
Last synced: 20 Feb 2025
https://github.com/bhklab/haloplexcnvpipeline
A Snakemake pipeline for calling CNVs from Haloplex Target Enrichment (targeted sequencing array) for samples without a matched normal.
Last synced: 20 Feb 2025
https://github.com/bhklab/metagxdata-pipeline
MetaGxData Packages Compedium
Last synced: 20 Feb 2025
https://github.com/bhklab/jakstat
PSet generation scripts for datasets shared by JAK STAT partners.
Last synced: 20 Feb 2025
https://github.com/bhklab/bhklab-test-project_src
An example of exactly what the template creates!
Last synced: 15 May 2025
https://github.com/bhklab/bhklab-test-project
An example of exactly what the template creates!
Last synced: 15 May 2025
https://github.com/bhklab/tissue-biomarker-pipeline
A pipeline to run meta-analysis of biomarkers in preclinical PGx data using Snakemake, R, Julia, and the cloud
Last synced: 15 May 2025
https://github.com/bhklab/public_image_data_curation
Code to collect info about publicly available medical image datasets for curation
Last synced: 15 May 2025
https://github.com/bhklab/lung-lesion-treatment-response-prediction
Code + Data for Lung Lesion Treatment Response Prediction
Last synced: 15 May 2025
https://github.com/bhklab/hnscc_clinical_data_handling
Preprocessing the clinical data from the HNSCC dataset on TCIA
Last synced: 23 Mar 2025
https://github.com/bhklab/ispy-readii
Running READII on the I-SPY cohort for radiogenomic analysis.
Last synced: 23 Mar 2025
https://github.com/bhklab/cdrug-rebuttal
Code for "Assessment of pharmacogenomic agreement" by Safikhani et al -> Response to "Pharmacogenomic agreement between two cancer cell line data sets" by the GDSC/CCLE investigators
Last synced: 20 Feb 2025