Predictive models and analysis of cancer prognosis and drug response using primary tumor microbial abundances derived from WGS and RNA-seq sequencing data for 32 TCGA cancers (Poore et al. Nature 2020), including equivalent models using TCGA RNA-seq gene expression and combined microbial abundance and gene expression for comparison.
☆18Nov 13, 2024Updated last year
Alternatives and similar repositories for tcga-microbiome-prediction
Users that are interested in tcga-microbiome-prediction are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- The code for running the analysis component of CSI-Microbe☆12Jan 3, 2024Updated 2 years ago
- Scripts and Data associated with our publication on genomic signatures to discriminate LUAD and LUSC lung cancer types using TCGA data☆11Mar 2, 2022Updated 4 years ago
- MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data☆18Jul 15, 2025Updated 9 months ago
- Code for the identification step for CSI-Microbes☆31Nov 25, 2024Updated last year
- Tumor type classifier using cancer genomic panel sequencing data☆13Mar 12, 2024Updated 2 years ago
- Serverless GPU API endpoints on Runpod - Bonus Credits • AdSkip the infrastructure headaches. Auto-scaling, pay-as-you-go, no-ops approach lets you focus on innovating your application.
- Microbial analysis in TCGA data☆94Feb 23, 2024Updated 2 years ago
- An R package to implement Differential Gene Set Enrichment Analysis (DGSEA): A statistical approach to quantify the relative enrichment o…☆14Apr 12, 2023Updated 3 years ago
- Integrating temporal gene expression modalities for trajectory inference and disease prediction☆10Sep 20, 2022Updated 3 years ago
- FOR my learing☆12Feb 19, 2026Updated 2 months ago
- Toolbox package for organizing and working with TCGA data☆28Mar 26, 2026Updated 3 weeks ago
- ☆18Oct 13, 2023Updated 2 years ago
- CRC Subtyping Consortium☆13Jun 1, 2018Updated 7 years ago
- meta-analysis of new and published human WAT single cell data☆15Mar 12, 2025Updated last year
- The Cancer bioMarker Prediction Pipeline (CAMPP)☆19Oct 25, 2020Updated 5 years ago
- Virtual machines for every use case on DigitalOcean • AdGet dependable uptime with 99.99% SLA, simple security tools, and predictable monthly pricing with DigitalOcean's virtual machines, called Droplets.
- Batch effects removal for microbiome data via conditional quantile regression☆32Aug 23, 2022Updated 3 years ago
- R package to use EaSIeR to predict anti-tumor immune response from bulk RNA-seq☆15Dec 1, 2025Updated 4 months ago
- Integrating LASSO and bootstrapping algorithm to find best prognostic or predictive biomarkers☆21Oct 12, 2022Updated 3 years ago
- code and data for Liu, Schilling, et al Nat Med 2019☆17Aug 1, 2024Updated last year
- The Moving Epidemic Method R Package☆17Oct 7, 2025Updated 6 months ago
- This repository contains computer codes for main analyses of the manuscript titled 'Multi-omic Landscape of Airway Microbe-Host Interacti…☆33Aug 16, 2022Updated 3 years ago
- ☆21Apr 16, 2024Updated 2 years ago
- Pipeline for the generation and simulation of personalized Flux Balance Analysis models☆11Feb 14, 2021Updated 5 years ago
- Immune Cell Gene Signatures for Profiling the Microenvironment of Solid Tumours☆28Jan 9, 2021Updated 5 years ago
- Managed Database hosting by DigitalOcean • AdPostgreSQL, MySQL, MongoDB, Kafka, Valkey, and OpenSearch available. Automatically scale up storage and focus on building your apps.
- This is a companion repository for the article "Comparative analysis of machine learning classifiers and calibration algorithms for estim…☆25Mar 22, 2022Updated 4 years ago
- This repository contains code for the evaluation of epithelial-to-mesenchymal transition states in cancer.☆13Jan 24, 2023Updated 3 years ago
- m(6)A methylation analysis☆10Mar 9, 2019Updated 7 years ago
- ☆33Jul 17, 2021Updated 4 years ago
- A lightweight and flexible analysis pipeline☆12Apr 9, 2026Updated last week
- ☆92Sep 3, 2024Updated last year
- CancerMIRNome - an interactive analysis and visualization database for miRNome profiles of human cancer☆12Aug 9, 2024Updated last year
- Non-parametric structural variant genotyper☆15Nov 18, 2021Updated 4 years ago
- Pan-cancer mycobiome atlas☆31Oct 7, 2022Updated 3 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Data-driven Network-based Bayesian Inference of Drivers☆48Aug 18, 2025Updated 8 months ago
- Time-stratified case-crossover studies for aggregated data in environmental epidemiology: a tutorial☆12Jul 25, 2025Updated 8 months ago
- 使用表达数据,对候选基因进行特征选择,然后构建诊断/预后模型,并使用SHAP分析特征的贡献策划的怒☆16Oct 16, 2025Updated 6 months ago
- An R package to fit dose response curves for data from the Genomics of Drug Sensitivity of Cancer (GDSC) project.☆28Jul 10, 2023Updated 2 years ago
- ☆28Sep 20, 2023Updated 2 years ago
- Readme☆10Mar 15, 2020Updated 6 years ago
- Ordering gene-expression and functional events in single-cell experiments☆30Mar 7, 2026Updated last month