scPred package for cell type prediction from scRNA-seq data
☆98Jan 18, 2024Updated 2 years ago
Alternatives and similar repositories for scPred
Users that are interested in scPred are comparing it to the libraries listed below
Sorting:
- R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets☆246Aug 18, 2025Updated 6 months ago
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆238May 8, 2023Updated 2 years ago
- MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell trans…☆182Aug 12, 2025Updated 6 months ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆313Nov 1, 2022Updated 3 years ago
- Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data☆41Nov 18, 2021Updated 4 years ago
- Methods to discover gene programs on single-cell data☆174Sep 26, 2025Updated 5 months ago
- AUCell: score single cells with gene regulatory networks☆185Mar 9, 2024Updated last year
- Metacell - Single-cell mRNA Analysis☆120Jan 26, 2025Updated last year
- marker-based purification of cell types from single-cell RNA-seq datasets☆141Jul 23, 2025Updated 7 months ago
- Automated cell type classification☆116Jan 3, 2025Updated last year
- ☆285Nov 10, 2024Updated last year
- Tools and methods for analysis of single cell assay data in R☆261Oct 17, 2025Updated 4 months ago
- Automated, probabilistic assignment of cell types in scRNA-seq data☆211Jan 9, 2023Updated 3 years ago
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆219Feb 26, 2024Updated 2 years ago
- R client for the OmniPath web service☆154Feb 12, 2026Updated 2 weeks ago
- Easy single cell analysis platform for enrichment☆214Jan 4, 2026Updated last month
- TRAjectory-based Differential Expression analysis for SEQuencing data☆290Jun 17, 2025Updated 8 months ago
- R package for detecting doublets in single-cell RNA sequencing data☆525Mar 21, 2025Updated 11 months ago
- Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.☆167Jan 8, 2026Updated last month
- Methods for detecting doublets in single-cell sequencing data☆231Feb 12, 2026Updated 2 weeks ago
- R package for modeling single cell UMI expression data using regularized negative binomial regression☆251Jan 10, 2026Updated last month
- A package to help convert different single-cell data formats to each other☆458Feb 20, 2026Updated last week
- Coarse-graining of large single-cell RNA-seq data into metacells☆94Updated this week
- Methods to compute Local Inverse Simpson's Index (LISI)☆75Sep 2, 2021Updated 4 years ago
- ☆99Sep 17, 2025Updated 5 months ago
- Scissor package☆252May 10, 2024Updated last year
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆322Jul 28, 2020Updated 5 years ago
- CosMx Spatial Molecular Imager-derived cell profiles to aid in cell typing of SMI data.☆34Jan 24, 2025Updated last year
- Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data☆153Aug 3, 2025Updated 6 months ago
- Python library for plotting Cellphonedb results. Ported from ktplots R package.☆57Updated this week
- R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.☆289Feb 18, 2026Updated last week
- Signature Analysis and Visualization for Single-Cell RNA-seq☆175Jun 10, 2024Updated last year
- R package to infer biological activities from omics data using a collection of methods.☆285Dec 16, 2025Updated 2 months ago
- Interpretation of cell states using reference single-cell maps☆312Dec 19, 2025Updated 2 months ago
- Inferring CNV from Single-Cell RNA-Seq☆651Nov 14, 2025Updated 3 months ago
- Multi-subject Single Cell Deconvolution☆286Mar 4, 2024Updated last year
- A tool for semi-automatic cell type classification☆453Updated this week
- NicheNet: predict active ligand-target links between interacting cells☆620Nov 12, 2025Updated 3 months ago
- Algorithms for single-cell analysis☆29Jul 19, 2021Updated 4 years ago