Scanpy use cases.
☆90Sep 4, 2020Updated 5 years ago
Alternatives and similar repositories for scanpy_usage
Users that are interested in scanpy_usage are comparing it to the libraries listed below
Sorting:
- Scanpy Tutorials.☆235Mar 9, 2026Updated last week
- Single-cell analysis in Python. Scales to >100M cells.☆2,367Mar 13, 2026Updated last week
- ☆69May 2, 2018Updated 7 years ago
- MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …☆379Oct 3, 2024Updated last year
- MAGIC - imputation and de-noising single-cell RNA seq data sets☆27Sep 19, 2019Updated 6 years ago
- Fit generalized linear models in python.☆28Mar 6, 2023Updated 3 years ago
- ☆20Mar 28, 2017Updated 8 years ago
- ☆19Oct 27, 2021Updated 4 years ago
- RNA Velocity generalized through dynamical modeling☆494Feb 25, 2026Updated 3 weeks ago
- ☆17Oct 3, 2022Updated 3 years ago
- Consistent Clusters for scRNA-seq☆11Oct 6, 2021Updated 4 years ago
- Human cortical cell types☆25Aug 21, 2019Updated 6 years ago
- A collection of project templates and useful functions for single-cell data analysis with Scanpy.☆21Jun 12, 2023Updated 2 years ago
- A collection of scripts and tools for loading, processing, and handling single cell data.☆77Sep 22, 2025Updated 5 months ago
- Episcanpy: Epigenomics Single Cell Analysis in Python☆150Dec 5, 2024Updated last year
- 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
- Single-cell Orientation Tracing☆22Jan 23, 2022Updated 4 years ago
- ☆35Nov 29, 2021Updated 4 years ago
- Use cases for anndata.☆14Jun 11, 2025Updated 9 months ago
- Exon-Intron Split Analysis (EISA) in R☆17Nov 3, 2025Updated 4 months ago
- Single cell perturbation prediction☆337Dec 5, 2024Updated last year
- Integrating zingeR with ZINB-WaVE weights☆26Feb 15, 2018Updated 8 years ago
- scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources…☆110Dec 16, 2022Updated 3 years ago
- Mapping out the coarse-grained connectivity structures of complex manifolds.☆237May 23, 2020Updated 5 years ago
- Panoramic stitching of single cell data☆297Jul 14, 2025Updated 8 months ago
- [Deprecated, see https://github.com/antigenomics/mirpy and other tools @antigenomics] Post-analysis of immune repertoire sequencing data☆143May 23, 2024Updated last year
- Normalization for single cell RNA-seq data☆51Jun 11, 2025Updated 9 months ago
- Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq an…☆1,556Dec 11, 2022Updated 3 years ago
- ☆57May 22, 2018Updated 7 years ago
- Scripts used for the Differential NicheNet analyses in the Liver Atlas paper Guilliams et al., Cell 2022☆10Jan 12, 2022Updated 4 years ago
- Algorithm for the inference of cell types and lineage trees from single-cell RNA-seq data.☆42Mar 3, 2017Updated 9 years ago
- Tools and methods for analysis of single cell assay data in R☆261Oct 17, 2025Updated 5 months ago
- main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datase…☆114Jan 20, 2023Updated 3 years ago
- An object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data☆52Jul 12, 2018Updated 7 years ago
- Scripts used for "Comparing transcriptional dynamics of the epithelial-mesenchymal transition"☆18Aug 1, 2023Updated 2 years ago
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆585Jun 26, 2025Updated 8 months ago
- Single-cell Scalable Visualization and Analytics☆27Mar 26, 2019Updated 6 years ago
- simpler single cell RNAseq data clustering☆43Feb 28, 2025Updated last year
- ☆16Nov 5, 2024Updated last year