Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".
☆132Sep 6, 2024Updated last year
Alternatives and similar repositories for 3ca
Users that are interested in 3ca are comparing it to the libraries listed below
Sorting:
- Code for major analyses in "Integrative spatial analysis reveals a multi-layered organization of glioblastoma" paper☆55Jan 6, 2025Updated last year
- ☆63Dec 27, 2023Updated 2 years ago
- Methods to discover gene programs on single-cell data☆176Sep 26, 2025Updated 5 months ago
- Data available at: https://www.dropbox.com/sh/jh4s57kgbb0rnxe/AABoMK466cGc1OKsOuFN10wca?dl=0 and https://nyulangone-my.sharepoint.com//g/…☆31Aug 17, 2022Updated 3 years ago
- Prostate Cancer Alteration Signature Analysis https://xsliulab.github.io/PC_CNA_signature/☆13May 17, 2021Updated 4 years ago
- Scissor package☆253May 10, 2024Updated last year
- Infer Copy Number Alterations and Clonality in (Single-Cell) RNA-Seq Data☆51Jan 12, 2024Updated 2 years ago
- EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.☆234Mar 28, 2024Updated last year
- Codes used in pan-T cell analysis☆65Mar 13, 2023Updated 3 years ago
- ☆17Mar 27, 2023Updated 2 years ago
- Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data☆419Aug 22, 2025Updated 7 months ago
- Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolu…☆65Dec 7, 2022Updated 3 years ago
- ☆33Feb 26, 2025Updated last year
- ☆16Nov 5, 2024Updated last year
- 🐯 tigeR: Tumor Immunotherapy Gene Expression Data Analysis R package☆54Jan 21, 2026Updated 2 months ago
- These are scripts for pan-cacner NK cells analyses.☆76Aug 18, 2023Updated 2 years ago
- STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)☆117Apr 26, 2025Updated 10 months ago
- Custom codes accompanying single cell spatial transcriptomic study on the healthy human lung☆13Dec 27, 2023Updated 2 years ago
- R code used to analyze single cell PDAC data☆42Jun 29, 2024Updated last year
- ☆22Mar 6, 2023Updated 3 years ago
- scRNA-seq analysis of EENT-ONB☆22Jan 14, 2024Updated 2 years ago
- ☆114Sep 16, 2020Updated 5 years ago
- ☆273Oct 13, 2025Updated 5 months ago
- Clone Calling from Visium Spatial Transcriptomics of Cancer samples☆91Dec 8, 2022Updated 3 years ago
- ☆17Sep 13, 2023Updated 2 years ago
- ☆58Feb 23, 2024Updated 2 years ago
- Lung cancer 10X analysis☆11Dec 30, 2020Updated 5 years ago
- CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.☆227Updated this week
- Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".☆128Sep 24, 2024Updated last year
- Repository for codes for the HBCA paper☆42Mar 17, 2023Updated 3 years ago
- Scripts used for the ACT paper☆12May 6, 2021Updated 4 years ago
- IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.☆280Mar 15, 2026Updated last week
- ☆28Jan 15, 2024Updated 2 years ago
- ☆57Aug 8, 2024Updated last year
- R package implementation of Milo for testing for differential abundance in KNN graphs☆423Sep 4, 2025Updated 6 months ago
- SNV calling from single cell sequencing☆119Nov 11, 2024Updated last year
- ☆129Mar 27, 2022Updated 3 years ago
- Inferring CNV from Single-Cell RNA-Seq☆660Nov 14, 2025Updated 4 months ago
- Single Cell Analysis Operations☆13Nov 25, 2025Updated 3 months ago