R package for modeling single cell UMI expression data using regularized negative binomial regression
☆267Jan 10, 2026Updated 7 months ago
Alternatives and similar repositories for sctransform
Users that are interested in sctransform are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆336Nov 1, 2022Updated 3 years ago
- R package for detecting doublets in single-cell RNA sequencing data☆557Mar 21, 2025Updated last year
- Interfaces for HDF5-based Single Cell File Formats☆178Nov 4, 2023Updated 2 years ago
- Clone of the Bioconductor repository for the SingleR package.☆204Jul 7, 2026Updated last month
- R package for integrating and analyzing multiple single-cell datasets☆432Feb 4, 2026Updated 6 months ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- TRAjectory-based Differential Expression analysis for SEQuencing data☆309Jun 17, 2025Updated last year
- Methods for detecting doublets in single-cell sequencing data☆259Jul 7, 2026Updated last month
- ☆463May 26, 2026Updated 2 months ago
- R toolkit for single cell genomics☆2,783Jul 14, 2026Updated 3 weeks ago
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆343Apr 23, 2024Updated 2 years ago
- Tools and methods for analysis of single cell assay data in R☆265Oct 17, 2025Updated 9 months ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆667Jun 5, 2026Updated 2 months ago
- Community-provided extensions to Seurat☆370Jun 29, 2026Updated last month
- Interpretation of cell states using reference single-cell maps☆323Dec 19, 2025Updated 7 months ago
- GPUs on demand by Runpod - Special Offer Available • AdRun AI, ML, and HPC workloads on powerful cloud GPUs—without limits or wasted spend. Deploy GPUs in under a minute and pay by the second.
- A Shiny web app for mapping datasets using Seurat v4☆150May 22, 2026Updated 2 months ago
- A toolkit for single-cell immune profiling☆374Jul 9, 2026Updated last month
- A tool for removing doublets from single-cell RNA-seq data☆75Dec 2, 2020Updated 5 years ago
- Multi-sample multi-group scRNA-seq analysis tools☆240Jul 6, 2026Updated last month
- R toolkit for the analysis of single-cell chromatin data☆424Updated this week
- Doublet detection in single-cell RNA-seq data.☆98Feb 6, 2025Updated last year
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆244May 8, 2023Updated 3 years ago
- Fast Wilcoxon and auROC☆216May 5, 2026Updated 3 months ago
- Easy single cell analysis platform for enrichment☆228Updated this week
- Wordpress hosting with auto-scaling - Free Trial Offer • AdFully Managed hosting for WordPress and WooCommerce businesses that need reliable, auto-scalable performance. Cloudways SafeUpdates now available.
- R package implementation of Milo for testing for differential abundance in KNN graphs☆442May 11, 2026Updated 2 months ago
- A package to help convert different single-cell data formats to each other☆470Feb 20, 2026Updated 5 months ago
- ☆364Dec 9, 2021Updated 4 years ago
- AUCell: score single cells with gene regulatory networks☆201Mar 9, 2024Updated 2 years ago
- NicheNet: predict active ligand-target links between interacting cells☆670Jun 1, 2026Updated 2 months ago
- Inferring CNV from Single-Cell RNA-Seq☆680Nov 14, 2025Updated 8 months ago
- Reference mapping for single-cell genomics☆407Jun 26, 2026Updated last month
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆230Jul 2, 2026Updated last month
- An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.☆178Jan 26, 2024Updated 2 years ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆494Apr 5, 2024Updated 2 years ago
- CellRank: dynamics from multi-view single-cell data☆454Aug 3, 2026Updated last week
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆347Jul 28, 2020Updated 6 years ago
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆631Jun 26, 2025Updated last year
- Bayesian Hierarchical Modeling for Clustering Single Cell Genomic Data☆155Jun 26, 2026Updated last month
- Coarse-graining of large single-cell RNA-seq data into metacells☆105Apr 16, 2026Updated 3 months ago
- Automated, probabilistic assignment of cell types in scRNA-seq data☆214Jan 9, 2023Updated 3 years ago