A robust DE test method that accounts for the uncertainty in pseudotime inference
☆40Mar 2, 2025Updated last year
Alternatives and similar repositories for PseudotimeDE
Users that are interested in PseudotimeDE are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- An interpretable simulator that generates realistic single-cell gene expression count data with gene correlations recapitulated☆30Nov 2, 2024Updated last year
- scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics☆123Sep 29, 2025Updated 10 months ago
- A post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping☆29Updated this week
- A single cell sequencing read simulator.☆34Oct 14, 2024Updated last year
- ☆15Jul 11, 2023Updated 3 years ago
- Managed Kubernetes at scale on DigitalOcean • AdDigitalOcean Kubernetes includes the control plane, bandwidth allowance, container registry, automatic updates, and more for free.
- ☆64Aug 26, 2025Updated 11 months ago
- Single-cell generalized trendmodel (scGTM): a flexible and interpretable model for gene expression along cell pseudotime. This is a Pyt…☆12Sep 26, 2023Updated 2 years ago
- ☆14Aug 13, 2023Updated 2 years ago
- scType goes spatial: ScType enables fast and accurate cell type identification from spatial transcriptomics data☆12Jul 11, 2024Updated 2 years ago
- ☆31Mar 18, 2022Updated 4 years ago
- Scripts to reproduce analyses of tradeSeq paper.☆16Feb 5, 2020Updated 6 years ago
- Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data☆11Jul 6, 2026Updated last month
- Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data☆42Nov 18, 2021Updated 4 years ago
- hJAM is a hierarchical model which unifies the framework of Mendelian Randomization and Transcriptome-wide association studies.☆11Jan 19, 2024Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click. Zero configuration with optimized deployments.
- ☆17Nov 13, 2021Updated 4 years ago
- Constructing gene regulatory networks by integrating scRNA-seq and scATAC-seq data☆13Dec 7, 2021Updated 4 years ago
- Automatic selection of number of principal components☆17Jun 27, 2022Updated 4 years ago
- A statistical simulator for rational scRNA-seq experimental design☆14Dec 14, 2020Updated 5 years ago
- Spatial RNA velocity☆10Oct 3, 2024Updated last year
- ☆14May 1, 2024Updated 2 years ago
- Framework for Unified Single-Cell Analysis (FUSCA) is a software package for single-cell data analysis developed in R. At the moment, it …☆22Feb 14, 2023Updated 3 years ago
- Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression☆32Dec 3, 2024Updated last year
- R package IReNA☆31Nov 13, 2024Updated last year
- 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.
- ☆12May 30, 2023Updated 3 years ago
- Analysis tool for NG-Capture-C, Tri-C and Tiled-C data☆10Jun 10, 2026Updated 2 months ago
- Non-parametric density inference for single-cell analysis.☆75Jul 28, 2026Updated 2 weeks ago
- model-based understanding of single-cell CRISPR screening☆29Dec 13, 2024Updated last year
- ☆10Jul 3, 2018Updated 8 years ago
- LACE 2.0 is a new release of the LACE R Bioconductor package, which provides an interactive user interface to perform clonal evolution an…☆16Apr 7, 2026Updated 4 months ago
- R package for normalisation of spatial transcriptomics data☆18Jul 27, 2026Updated 2 weeks ago
- Python implementation of Gene Trajectory☆30Sep 4, 2024Updated last year
- Global Waddington-OT☆23Mar 25, 2025Updated last year
- Deploy to Railway using AI coding agents - Free Credits Offer • AdUse Claude Code, Codex, OpenCode, and more. Autonomous software development now has the infrastructure to match with Railway.
- All code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs☆42Mar 20, 2023Updated 3 years ago
- BioTIP: Biological Tipping-Point Identification and Characterization☆24Oct 20, 2025Updated 9 months ago
- Processing workflow for COVID-19 single cell data☆17Dec 23, 2021Updated 4 years ago
- A portable and fast single cell type identifier☆64May 12, 2021Updated 5 years ago
- Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)☆34Feb 22, 2018Updated 8 years ago
- scVI extension for unspliced RNA☆15May 18, 2025Updated last year
- ☆14Jul 28, 2023Updated 3 years ago