☆293Jul 15, 2022Updated 3 years ago
Alternatives and similar repositories for monocle-release
Users that are interested in monocle-release are comparing it to the libraries listed below
Sorting:
- ☆442Jan 8, 2026Updated last month
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆323Jul 28, 2020Updated 5 years ago
- R package for analyzing single-cell RNA-seq data☆179Feb 29, 2024Updated 2 years ago
- R toolkit for single cell genomics☆2,661Feb 20, 2026Updated 2 weeks ago
- Tools and methods for analysis of single cell assay data in R☆261Oct 17, 2025Updated 4 months ago
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆477Apr 5, 2024Updated last year
- ☆360Dec 9, 2021Updated 4 years ago
- scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources…☆110Dec 16, 2022Updated 3 years ago
- R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets☆246Aug 18, 2025Updated 6 months ago
- Fast, sensitive and accurate integration of single-cell data with Harmony☆622Oct 10, 2025Updated 4 months ago
- R package for detecting doublets in single-cell RNA sequencing data☆526Mar 21, 2025Updated 11 months ago
- An R-based interface for loom files☆67Jul 9, 2020Updated 5 years ago
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.☆324Apr 23, 2024Updated last year
- Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕☆185Jun 24, 2021Updated 4 years ago
- AUCell: score single cells with gene regulatory networks☆185Mar 9, 2024Updated last year
- Analysis Pipeline for Single Cell ATAC-seq☆321Apr 27, 2023Updated 2 years ago
- Inferring CNV from Single-Cell RNA-Seq☆653Nov 14, 2025Updated 3 months ago
- NicheNet: predict active ligand-target links between interacting cells☆620Nov 12, 2025Updated 3 months ago
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)☆447Feb 18, 2025Updated last year
- R package for integrating and analyzing multiple single-cell datasets☆424Feb 4, 2026Updated last month
- Probabilistic pseudotime for single-cell RNA-seq data☆10Oct 6, 2017Updated 8 years ago
- RNA velocity estimation in Python☆175Oct 7, 2025Updated 5 months ago
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.☆3,668Updated this week
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆579Jun 26, 2025Updated 8 months ago
- STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data☆179Dec 18, 2021Updated 4 years ago
- chromatin Variability Across Regions (of the genome!)☆185Jul 10, 2024Updated last year
- Single-cell Transcriptome and Regulome Analysis Pipeline☆303Mar 6, 2023Updated 3 years ago
- MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …☆379Oct 3, 2024Updated last year
- RNA Velocity generalized through dynamical modeling☆491Feb 25, 2026Updated last week
- ☆59Sep 3, 2024Updated last year
- R package for modeling single cell UMI expression data using regularized negative binomial regression☆251Jan 10, 2026Updated last month
- ☆69May 2, 2018Updated 7 years ago
- Single-cell analysis in Python. Scales to >100M cells.☆2,362Updated this week
- Interactively analyze single cell genomic data☆185Jan 14, 2026Updated last month
- Fast Wilcoxon and auROC☆204Nov 8, 2024Updated last year
- Analysis of single cell RNA-seq data course☆680Apr 11, 2022Updated 3 years ago
- Community-provided extensions to Seurat☆358Feb 17, 2026Updated 2 weeks ago
- A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments☆129Jun 28, 2021Updated 4 years ago
- URD - Reconstruction of Branching Developmental Trajectories☆126Jun 29, 2021Updated 4 years ago