An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
β443Aug 12, 2026Updated 3 weeks ago
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.β3,848Updated this week
- A collection of 50+ trajectory inference methods within a common interface π₯π€β131Dec 21, 2023Updated 2 years ago
- Table of software for the analysis of single-cell RNA-seq data.β344Updated this week
- Comparison of methods for trajectory inference on single-cell data π₯β222Aug 30, 2023Updated 3 years ago
- Panoramic stitching of single cell dataβ294Jul 14, 2025Updated last year
- End-to-end encrypted cloud storage - Proton Drive β’ AdSpecial offer: 40% Off Yearly / 80% Off First Month. Protect your most important files, photos, and documents from prying eyes.
- CellRank: dynamics from multi-view single-cell dataβ456Aug 31, 2026Updated last week
- This is the alpha version of the CellOracle packageβ491Apr 30, 2026Updated 4 months ago
- A list of scRNA-seq analysis toolsβ814Jul 29, 2026Updated last month
- Deep probabilistic analysis of single-cell and spatial omics dataβ1,683Updated this week
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.β497Apr 5, 2024Updated 2 years ago
- Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction β¦β509Jul 26, 2026Updated last month
- Functions for identifying and characterizing continuous developmental trajectories in single-cell data.β347Apr 23, 2024Updated 2 years ago
- trajectory inferenceβ109Jan 27, 2025Updated last year
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) whichβ¦β635Jun 26, 2025Updated last year
- AI Agents on DigitalOcean Gradient AI Platform β’ AdBuild production-ready AI agents using customizable tools or access multiple LLMs through a single endpoint. Create custom knowledge bases or connect external data.
- Multi-omic velocity inferenceβ120Oct 23, 2024Updated last year
- TRAjectory-based Differential Expression analysis for SEQuencing dataβ311Jun 17, 2025Updated last year
- A package to help convert different single-cell data formats to each otherβ470Feb 20, 2026Updated 6 months ago
- Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq anβ¦β1,591Dec 11, 2022Updated 3 years ago
- Collections of library structure and sequence of popular single cell genomic methodsβ509Apr 16, 2026Updated 4 months ago
- Analysis of single cell RNA-seq data courseβ683Apr 11, 2022Updated 4 years ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq dataβ342Nov 1, 2022Updated 3 years ago
- scRNAseq analysis notes from Ming Tangβ833Dec 2, 2024Updated last year
- Single-cell analysis in Python. Scales to >100M cells.β2,551Updated this week
- Deploy open-source AI quickly and easily - Special Bonus Offer β’ AdRunpod Hub is built for open source. One-click deployment and autoscaling endpoints without provisioning your own infrastructure.
- R toolkit for single cell genomicsβ2,795Updated this week
- Analysis Pipeline for Single Cell ATAC-seqβ321Apr 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¦β112Dec 16, 2022Updated 3 years ago
- Batch balanced KNNβ180Oct 11, 2023Updated 2 years ago
- Reference mapping for single-cell genomicsβ407Jun 26, 2026Updated 2 months ago
- NicheNet: predict active ligand-target links between interacting cellsβ674Jun 1, 2026Updated 3 months ago
- Automated, probabilistic assignment of cell types in scRNA-seq dataβ215Jan 9, 2023Updated 3 years ago
- RNA Velocity generalized through dynamical modelingβ511Feb 25, 2026Updated 6 months ago
- ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)β464Feb 18, 2025Updated last year
- Proton VPN Special Offer - Get 70% off β’ AdSpecial partner offer. Trusted by over 100 million users worldwide. Tested, Approved and Recommended by Experts.
- Mapping out the coarse-grained connectivity structures of complex manifolds.β244May 23, 2020Updated 6 years ago
- Inferring, interpreting and visualising trajectories using a streamlined set of packages π¦β187Jun 24, 2021Updated 5 years ago
- This contains the dataset for comparing scRNA-seq analysis methodsβ93Aug 26, 2020Updated 6 years ago
- R package for integrating and analyzing multiple single-cell datasetsβ432Aug 18, 2026Updated 2 weeks ago
- STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell dataβ184Dec 18, 2021Updated 4 years ago
- Single cell trajectory detectionβ333Jul 15, 2026Updated last month
- ACTIONet single-cell analysis frameworkβ47Aug 28, 2026Updated last week