A robust DE test method that accounts for the uncertainty in pseudotime inference
☆39Mar 2, 2025Updated last year
Alternatives and similar repositories for PseudotimeDE
Users that are interested in PseudotimeDE are comparing it to the libraries listed below
Sorting:
- A post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping☆28Dec 11, 2025Updated 3 months ago
- An interpretable simulator that generates realistic single-cell gene expression count data with gene correlations recapitulated☆27Nov 2, 2024Updated last year
- scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics☆116Sep 29, 2025Updated 5 months ago
- A single cell sequencing read simulator.☆34Oct 14, 2024Updated last year
- ☆13Jul 11, 2023Updated 2 years ago
- ☆63Aug 26, 2025Updated 6 months ago
- ☆14Aug 13, 2023Updated 2 years ago
- ☆27Mar 18, 2022Updated 4 years ago
- Scripts to reproduce analyses of tradeSeq paper.☆16Feb 5, 2020Updated 6 years ago
- scType goes spatial: ScType enables fast and accurate cell type identification from spatial transcriptomics data☆11Jul 11, 2024Updated last year
- 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
- Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data☆11Jul 11, 2024Updated last year
- Nuclear fraction QC metric to detect empty droplets and damaged cells in scRNA-seq data☆41Nov 18, 2021Updated 4 years ago
- ☆17Nov 13, 2021Updated 4 years ago
- Constructing gene regulatory networks by integrating scRNA-seq and scATAC-seq data☆13Dec 7, 2021Updated 4 years ago
- A statistical simulator for rational scRNA-seq experimental design☆12Dec 14, 2020Updated 5 years ago
- hJAM is a hierarchical model which unifies the framework of Mendelian Randomization and Transcriptome-wide association studies.☆10Jan 19, 2024Updated 2 years ago
- ☆14May 1, 2024Updated last year
- Trajectory inference across multiple conditions with condiments: differential topology, progression, differentiation, and expression☆29Dec 3, 2024Updated last year
- Spatial RNA velocity☆10Oct 3, 2024Updated last year
- 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
- R package IReNA☆29Nov 13, 2024Updated last year
- Automatic selection of number of principal components☆17Jun 27, 2022Updated 3 years ago
- Code repository for macsGESTALT single cell lineage tracing analysis https://doi.org/10.1101/2020.08.11.245787☆10May 10, 2021Updated 4 years ago
- Analysis tool for NG-Capture-C, Tri-C and Tiled-C data☆10Oct 13, 2025Updated 5 months ago
- Non-parametric density inference for single-cell analysis.☆73Mar 14, 2026Updated last week
- model-based understanding of single-cell CRISPR screening☆27Dec 13, 2024Updated last year
- R package for normalisation of spatial transcriptomics data☆17Jan 21, 2026Updated 2 months ago
- Python implementation of Gene Trajectory☆30Sep 4, 2024Updated last year
- LACE 2.0 is a new release of the LACE R Bioconductor package, which provides an interactive user interface to perform clonal evolution an…☆15Mar 9, 2026Updated last week
- ☆11May 30, 2023Updated 2 years ago
- Global Waddington-OT☆23Mar 25, 2025Updated 11 months ago
- Enformer Celltyping is a tensorflow, multi-headed attention based model that incorporates distal effects of Deoxyribonucleic Acid (DNA) i…☆16Jun 25, 2025Updated 8 months ago
- All code associated with manuscript detailing scATAC and scRNA-seq following stimulus of PBMCs☆41Mar 20, 2023Updated 3 years ago
- Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)☆32Feb 22, 2018Updated 8 years ago
- ☆16Jun 17, 2021Updated 4 years ago
- A portable and fast single cell type identifier☆64May 12, 2021Updated 4 years ago
- Take command of your set enrichment analyses.☆23Updated this week
- scVI extension for unspliced RNA☆16May 18, 2025Updated 10 months ago