Framework for clustering, phenotyping, pseudotiming and inferring gene regulatory networks from single cell data
☆109Jul 3, 2023Updated 2 years ago
Alternatives and similar repositories for bigSCale2
Users that are interested in bigSCale2 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- ☆56Dec 13, 2020Updated 5 years ago
- R markdown notebooks for the Tabula Muris network analysis in Iacono et al. (2019)☆12Jun 30, 2021Updated 4 years ago
- Single-cell Transcriptome and Regulome Analysis Pipeline☆306Mar 6, 2023Updated 3 years ago
- iCellR is an interactive R package designed to facilitate the analysis and visualization of high-throughput single-cell sequencing data. …☆128Nov 10, 2025Updated 4 months ago
- Multi-sample multi-group scRNA-seq analysis tools☆221Mar 8, 2026Updated 2 weeks ago
- Gene regulatory network reconstruction from pseudotemporal single-cell gene expression data☆11Jul 11, 2024Updated last year
- ☆11Jan 7, 2020Updated 6 years ago
- STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data☆180Dec 18, 2021Updated 4 years ago
- Reproducibility for the "Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models" paper☆13Jul 15, 2022Updated 3 years ago
- R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data☆317Nov 1, 2022Updated 3 years ago
- Imputation of single cell RNA-sequencing data with autoencoder☆16Jun 23, 2021Updated 4 years ago
- Analysis Pipeline for Single Cell ATAC-seq☆322Apr 27, 2023Updated 2 years ago
- Dynamic models for single-cell RNA-seq time series.☆40Sep 24, 2018Updated 7 years ago
- ☆48Jun 21, 2019Updated 6 years ago
- Comparison of dimensionality reduction methods☆30Mar 24, 2020Updated 6 years ago
- SAFE (Single-cell Aggregated clustering From Ensemble): Cluster ensemble for single-cell RNA-seq data☆18Mar 27, 2021Updated 4 years ago
- R package for integrating and analyzing multiple single-cell datasets☆427Feb 4, 2026Updated last month
- Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data. This is a novel R package of the RaceID3 and S…☆44Nov 25, 2024Updated last year
- SingleR: Single-cell RNA-seq cell types Recognition (legacy version)☆331Jul 28, 2020Updated 5 years ago
- Ordering gene-expression and functional events in single-cell experiments☆29Mar 7, 2026Updated 2 weeks ago
- Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data☆238May 8, 2023Updated 2 years ago
- Calculation of Reference/Cluster Similarity Spectrum (RSS/CSS)☆40Mar 6, 2024Updated 2 years ago
- A package to help convert different single-cell data formats to each other☆460Feb 20, 2026Updated last month
- NicheNet: predict active ligand-target links between interacting cells☆630Nov 12, 2025Updated 4 months ago
- netNMF-sc: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data☆23Apr 19, 2021Updated 4 years ago
- Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕☆185Jun 24, 2021Updated 4 years ago
- Mapping out the coarse-grained connectivity structures of complex manifolds.☆237May 23, 2020Updated 5 years ago
- Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…☆1,559Dec 11, 2022Updated 3 years ago
- R package for the joint analysis of multiple single-cell RNA-seq datasets☆220Mar 9, 2026Updated 2 weeks ago
- R package for modeling single cell UMI expression data using regularized negative binomial regression☆252Jan 10, 2026Updated 2 months ago
- TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data☆135Nov 28, 2023Updated 2 years ago
- SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.☆479Apr 5, 2024Updated last year
- Predicted cell-cell interactions of the aging mouse brain☆20Sep 24, 2019Updated 6 years ago
- Detect doublets in single-cell RNA-seq data☆86Jul 3, 2019Updated 6 years ago
- Single Cell RNA-seq UMI Filtering Facilitator☆10Oct 6, 2025Updated 5 months ago
- Discovering novel cell types across heterogenous single-cell experiments☆123Dec 8, 2022Updated 3 years ago
- Efficient and precise single-cell reference atlas mapping with Symphony☆114Oct 31, 2025Updated 4 months ago
- Automated cell type classification☆116Jan 3, 2025Updated last year
- Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)☆34Oct 6, 2022Updated 3 years ago