A unified interface to immune deconvolution methods (CIBERSORT, EPIC, quanTIseq, TIMER, xCell, MCPcounter) and mouse deconvolution methods
☆521Jan 5, 2026Updated last month
Alternatives and similar repositories for immunedeconv
Users that are interested in immunedeconv are comparing it to the libraries listed below
Sorting:
- Cell types enrichment analysis☆206May 27, 2024Updated last year
- IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.☆276Jan 3, 2026Updated 2 months ago
- Unified access to several second-generation deconvolution methods☆95Jan 5, 2026Updated last month
- Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)☆311Feb 10, 2026Updated 3 weeks ago
- Reproducible pipeline for "Comprehensive evaluation of cell-type quantification methods for immuno-oncology", Sturm et al. 2019, https://…☆44Jul 6, 2020Updated 5 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
- Scissor package☆253May 10, 2024Updated last year
- 🧬 immunarch [R package] – Multi-Modal Immune Repertoire Analytics for Immunotherapy and Vaccine Design☆338Nov 18, 2025Updated 3 months ago
- Inferring CNV from Single-Cell RNA-Seq☆653Nov 14, 2025Updated 3 months ago
- R package implementation of Milo for testing for differential abundance in KNN graphs☆421Sep 4, 2025Updated 6 months ago
- A toolkit for single-cell immune profiling☆363Updated this week
- Interpretation of cell states using reference single-cell maps☆312Dec 19, 2025Updated 2 months ago
- TCR and BCR assembly from RNA-seq data☆339Jan 22, 2026Updated last month
- Multi-subject Single Cell Deconvolution☆286Mar 4, 2024Updated last year
- Gene set variation analysis☆231Updated this week
- A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression☆226May 29, 2025Updated 9 months ago
- TRAjectory-based Differential Expression analysis for SEQuencing data☆290Jun 17, 2025Updated 8 months ago
- R package to infer biological activities from omics data using a collection of methods.☆286Dec 16, 2025Updated 2 months ago
- High dimensional weighted gene co-expression network analysis☆465Feb 13, 2026Updated 2 weeks ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆313Nov 1, 2022Updated 3 years ago
- R toolkit for inference, visualization and analysis of cell-cell communication from single-cell data☆765Jan 6, 2024Updated 2 years ago
- Some tools for plotting single-cell data☆178May 17, 2025Updated 9 months ago
- 🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R htt…☆158Dec 25, 2025Updated 2 months ago
- Easy single cell analysis platform for enrichment☆215Jan 4, 2026Updated last month
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆238May 8, 2023Updated 2 years ago
- Haplotype-aware CNV analysis from single-cell RNA-seq, ATAC-seq, and multiome☆205Feb 4, 2026Updated last month
- R package for integrating and analyzing multiple single-cell datasets☆424Feb 4, 2026Updated last month
- R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.☆289Updated this week
- R package for detecting doublets in single-cell RNA sequencing data☆525Mar 21, 2025Updated 11 months ago
- A unified interface to spatial transcriptomics deconvolution tools☆45Feb 15, 2026Updated 2 weeks ago
- Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.☆84Jul 12, 2023Updated 2 years ago
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆323Jul 28, 2020Updated 5 years ago
- Multi-sample multi-group scRNA-seq analysis tools☆218Feb 16, 2026Updated 2 weeks ago
- Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.☆181Feb 23, 2026Updated last week
- NicheNet: predict active ligand-target links between interacting cells☆620Nov 12, 2025Updated 3 months ago
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,659Feb 15, 2026Updated 2 weeks ago
- TIGS (Tumor Immunogenicity Score) project https://doi.org/10.7554/eLife.49020☆33Sep 16, 2021Updated 4 years ago
- STARTRAC(Single T-cell Analysis by Rna-seq and Tcr TRACking)☆117Apr 26, 2025Updated 10 months ago
- marker-based purification of cell types from single-cell RNA-seq datasets☆141Jul 23, 2025Updated 7 months ago