GitHub topics: tumor-heterogeneity
lima1/PureCN
Copy number calling and variant classification using targeted short read sequencing
Language: R - Size: 19 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 134 - Forks: 33
HautaniemiLab/jellyfisher
R htmlwidget for Jellyfish
Language: R - Size: 2.45 MB - Last synced at: 9 days ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 0
AntonioDeFalco/SCEVAN
R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.
Language: HTML - Size: 63 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 100 - Forks: 25
HautaniemiLab/jellyfish
Jellyfish plots for integrative visualization of spatio-temporal tumor evolution and clonal dynamics
Language: TypeScript - Size: 533 KB - Last synced at: 8 days ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 0
gavinha/TitanCNA
Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
Language: R - Size: 10.6 MB - Last synced at: 14 days ago - Pushed at: almost 4 years ago - Stars: 97 - Forks: 36
RichardObi/ccnet
Official repository of "Towards Learning Contrast Kinetics with Multi-Condition Latent Diffusion Models"
Language: Python - Size: 30.3 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 1
ChongQingNoSubway/DGR-MIL
Code for paper: DGR-MIL: Exploring Diverse Global Representation in Multiple Instance Learning for Whole Slide Image Classification [ECCV 2024]
Language: Python - Size: 2.29 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 128 - Forks: 4
its-Pa1/2D_Hypoxia_Modeling
This repository contains the codes for the article: Data-driven mechanistic modeling of oxygen distribution and hypoxia profile in tumor microenvironment
Language: MATLAB - Size: 147 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0
paoloinglese/ion_colocalization
Scripts used for the paper Inglese, P., Correia, G., Pruski, P., Glen, R. C., & Takats, Z. (2019). Colocalization features for classification of tumors using desorption electrospray ionization mass spectrometry imaging. Analytical chemistry.
Language: R - Size: 68.4 KB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0
emosca-cnr/scMuffin
scMuffin - A MUlti-Features INtegrative approach for SC data analysis
Language: R - Size: 78.3 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 0
KChen-lab/SiFit
Reconstructing phylogenetic tree from noisy mutation profile of single cells
Size: 24.7 MB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 2 - Forks: 2
cansysbio/HGSOC_TME_Heterogeneity
Analysis of treatment naive and neo-adjuvant chemotherapy treated high-grade serous ovarian cancer samples
Language: Jupyter Notebook - Size: 132 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 5 - Forks: 5
CMUSchwartzLab/BrM-Phylo
Phylogenies of Breast Cancer Brain Metastases
Language: Python - Size: 5.17 MB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 3 - Forks: 0
zhouzilu/DENDRO
Genetic Heterogeneity Profiling by Single Cell RNA Sequencing
Language: R - Size: 20.5 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 30 - Forks: 6
nriddiford/svSupport
A tool to find reads supporting/opposing structural variant breakpoints
Language: Python - Size: 2.57 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 1
jasa-acs/Bayesian-Hierarchical-Varying-sparsity-Regression-Models-with-Application-to-Cancer-Proteogenomics
Reproducibility materials for "Bayesian Hierarchical Varying-sparsity Regression Models with Application to Cancer Proteogenomics" by Yang Ni, Francesco C. Stingo, Min Jin Ha, Rehan Akbani & Veerabhadran Baladandayuthapani
Language: Matlab - Size: 157 KB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 2
munozalexander/Tumor-Heterogeneity
Assessing tumor heterogeneity in bulk tumor DNA. Simulation of reads from a phylogenetic prior.
Language: Jupyter Notebook - Size: 13.1 MB - Last synced at: over 1 year ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0
algo-cancer/PhISCS-BnB
A Fast Branch and Bound Algorithm for the Perfect Tumor Phylogeny Reconstruction Problem
Language: Python - Size: 11.8 MB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 8 - Forks: 3
FunGeST/Palimpsest
An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
Language: R - Size: 58.2 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 67 - Forks: 19
CMUSchwartzLab/RAD
Robust and Accurate Deconvolution
Language: Jupyter Notebook - Size: 111 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 9 - Forks: 2
ratschlab/secedo
Clustering tumor cells based on SNVs from single-cell sequencing data
Language: C++ - Size: 9.21 MB - Last synced at: almost 2 years ago - Pushed at: almost 3 years ago - Stars: 6 - Forks: 0
spectre-team/spectre 📦
This project provides an Spectre's implementation of Data Mining Group's algorithms for processing mass spectrometry imaging (MSI) datasets.
Language: TypeScript - Size: 125 MB - Last synced at: over 1 year ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 1
zengliX/SIFA
SIFA: identify tumor subclones and infer phylogenetic tree from WGS data
Language: R - Size: 2.16 MB - Last synced at: about 2 years ago - Pushed at: almost 7 years ago - Stars: 3 - Forks: 0
KChen-lab/Texomer
Texomer: Integrating Analysis of Cancer Genome and Transcriptome Sequencing Data
Language: R - Size: 32.9 MB - Last synced at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 19 - Forks: 8
danieldanciu/secedo-experiments
Experiments for evaluating SECEDO, clustering tumor cells based on single cell sequencing data
Language: Jupyter Notebook - Size: 207 KB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0
mostafa20223/GP
This repo is for "Tumor Heterogeneity - Graduation Project"
Language: Jupyter Notebook - Size: 409 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
alexandrutomescu/SNV-PPILP
Refined SNV calling for tumor data using perfect phylogenies and ILP
Language: Python - Size: 2.15 MB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0
