Papers with code for single cell related papers
☆316Mar 23, 2026Updated 5 months ago
Alternatives and similar repositories for single-cell-papers-with-code
Users that are interested in single-cell-papers-with-code are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.☆675Mar 11, 2026Updated 6 months ago
- ☆22Mar 6, 2023Updated 3 years ago
- Machine learning-based integrative analysis develops an immune-derived lncRNA signature for improving clinical outcomes in colorectal can…☆134May 30, 2025Updated last year
- Useful functions to make your scRNA-seq plot more cool!☆400Apr 18, 2026Updated 5 months ago
- Accurate and fast cell marker gene identification with COSG☆66Aug 25, 2026Updated 3 weeks ago
- End-to-end encrypted cloud storage - Proton Drive • AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.☆1,205Updated this week
- Single-cell multi-omics analysis reveals regulatory programs in clear cell renal cell carcinoma☆80Oct 29, 2024Updated last year
- Scissor package☆276May 10, 2024Updated 2 years ago
- CytoTRACE 2 is an interpretable AI method for predicting cellular potency and absolute developmental potential from scRNA-seq data.☆266Jul 8, 2026Updated 2 months ago
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,857Sep 7, 2026Updated last week
- https://www.sc-best-practices.org☆1,267Aug 29, 2026Updated 3 weeks ago
- Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…☆1,593Dec 11, 2022Updated 3 years ago
- Generate high quality, publication ready visualizations for single cell transcriptomics data.☆246Mar 2, 2026Updated 6 months ago
- ☆130Sep 4, 2025Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- ☆672Aug 20, 2026Updated 3 weeks ago
- IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology. https://iobr.github.…☆293Jul 23, 2026Updated last month
- Methods to discover gene programs on single-cell data☆210Updated this week
- Multi-Omics integration and VIsualization in Cancer Subtyping☆150Jul 19, 2021Updated 5 years ago
- Use batch balanced KNN (BBKNN) in R☆14Sep 9, 2025Updated last year
- Single-cell Lung Cancer Atlas with 1.2M cells☆94Jan 19, 2025Updated last year
- Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".☆139Sep 6, 2024Updated 2 years ago
- This is the repository that contains the analysis of the lung adenocarcinoma single cell dataset☆156Jan 6, 2021Updated 5 years ago
- A computational method to rank and infer drug-responsive cell population towards in-silico drug perturbation using a target-perturbed gen…☆76Oct 16, 2025Updated 11 months ago
- Simple, predictable pricing with DigitalOcean hosting • AdAlways know what you'll pay with monthly caps and flat pricing. Enterprise-grade infrastructure trusted by 600k+ customers.
- These are scripts for pan-cacner NK cells analyses.☆76Aug 18, 2023Updated 3 years ago
- 🐯 tigeR: Tumor Immunotherapy Gene Expression Data Analysis R package☆53Jan 21, 2026Updated 7 months ago
- A R package for advanced single cell data viz☆74Aug 29, 2025Updated last year
- Coarse-graining of large single-cell RNA-seq data into metacells☆110Apr 16, 2026Updated 5 months ago
- R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.☆311Jun 30, 2026Updated 2 months ago
- Quantifying metabolism activity at the single-cell resolution☆196Aug 20, 2026Updated 3 weeks ago
- An R package to calculate Dynamical Network Biomarkers (DNB).☆11Sep 16, 2022Updated 4 years ago
- ☆45May 3, 2021Updated 5 years ago
- High dimensional weighted gene co-expression network analysis☆494Jun 16, 2026Updated 3 months ago
- Managed hosting for WordPress and PHP on Cloudways • AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- A package to help convert different single-cell data formats to each other☆470Feb 20, 2026Updated 6 months ago
- ☆17Mar 6, 2024Updated 2 years ago
- Draw phylogenetic trees of tumor evolution☆87Jul 21, 2023Updated 3 years ago
- This repository contains the code used to generate figures and perform analysis for the manuscript titled "Transcriptomic and Spatial Pro…☆96Oct 9, 2024Updated last year
- Code for major analyses in "Integrative spatial analysis reveals a multi-layered organization of glioblastoma" paper☆57Jan 6, 2025Updated last year
- This repo is not maintained anymore, please refer to: https://github.com/rnacentre/BrainCellAtlas_reproducibility.☆17Sep 24, 2024Updated last year
- CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.☆486Jun 6, 2025Updated last year