An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
β439Apr 28, 2026Updated last week
Alternatives and similar repositories for single-cell-pseudotime
Users that are interested in single-cell-pseudotime are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.β3,722Updated this week
- A collection of 50+ trajectory inference methods within a common interface π₯π€β132Dec 21, 2023Updated 2 years ago
- Table of software for the analysis of single-cell RNA-seq data.β342Apr 30, 2026Updated last week
- Comparison of methods for trajectory inference on single-cell data π₯β221Aug 30, 2023Updated 2 years ago
- Panoramic stitching of single cell dataβ295Jul 14, 2025Updated 9 months ago
- Deploy on Railway without the complexity - Free Credits Offer β’ AdConnect your repo and Railway handles the rest with instant previews. Quickly provision container image services, databases, and storage volumes.
- CellRank: dynamics from multi-view single-cell dataβ443Updated this week
- This is the alpha version of the CellOracle packageβ448Apr 30, 2026Updated last week
- A list of scRNA-seq analysis toolsβ788Updated this week
- Deep probabilistic analysis of single-cell and spatial omics dataβ1,613Apr 30, 2026Updated last week
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.β482Apr 5, 2024Updated 2 years ago
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction β¦β492Apr 23, 2026Updated 2 weeks ago
- trajectory inferenceβ109Jan 27, 2025Updated last year
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.β328Apr 23, 2024Updated 2 years ago
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) whichβ¦β601Jun 26, 2025Updated 10 months ago
- Deploy to Railway using AI coding agents - Free Credits Offer β’ AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- Multi-omic velocity inferenceβ118Oct 23, 2024Updated last year
- TRAjectory-based Differential Expression analysis for SEQuencing dataβ295Jun 17, 2025Updated 10 months ago
- A package to help convert different single-cell data formats to each otherβ465Feb 20, 2026Updated 2 months ago
- Collections of library structure and sequence of popular single cell genomic methodsβ497Apr 16, 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 anβ¦β1,564Dec 11, 2022Updated 3 years ago
- Analysis of single cell RNA-seq data courseβ679Apr 11, 2022Updated 4 years ago
- scRNAseq analysis notes from Ming Tangβ804Dec 2, 2024Updated last year
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq dataβ324Nov 1, 2022Updated 3 years ago
- Single-cell analysis in Python. Scales to >100M cells.β2,441Updated this week
- Managed hosting for WordPress and PHP on Cloudways β’ AdManaged hosting for WordPress, Magento, Laravel, or PHP apps, on multiple cloud providers. Deploy in minutes on Cloudways by DigitalOcean.
- Analysis Pipeline for Single Cell ATAC-seqβ322Apr 27, 2023Updated 3 years ago
- scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sourcesβ¦β110Dec 16, 2022Updated 3 years ago
- Batch balanced KNNβ178Oct 11, 2023Updated 2 years ago
- R toolkit for single cell genomicsβ2,718May 1, 2026Updated last week
- Reference mapping for single-cell genomicsβ404Mar 21, 2026Updated last month
- This contains the dataset for comparing scRNA-seq analysis methodsβ93Aug 26, 2020Updated 5 years ago
- Mapping out the coarse-grained connectivity structures of complex manifolds.β241May 23, 2020Updated 5 years ago
- RNA Velocity generalized through dynamical modelingβ497Feb 25, 2026Updated 2 months ago
- Automated, probabilistic assignment of cell types in scRNA-seq dataβ213Jan 9, 2023Updated 3 years ago
- Managed Kubernetes at scale on DigitalOcean β’ AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- NicheNet: predict active ligand-target links between interacting cellsβ642Nov 12, 2025Updated 5 months ago
- R package for integrating and analyzing multiple single-cell datasetsβ429Feb 4, 2026Updated 3 months ago
- Inferring, interpreting and visualising trajectories using a streamlined set of packages π¦β185Jun 24, 2021Updated 4 years ago
- Single cell trajectory detectionβ309Apr 21, 2026Updated 2 weeks ago
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)β450Feb 18, 2025Updated last year
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)β335Jul 28, 2020Updated 5 years ago
- R package implementation of Milo for testing for differential abundance in KNN graphsβ429Apr 27, 2026Updated last week