Notebooks used in scvi-tools tutorials
☆62Feb 26, 2026Updated this week
Alternatives and similar repositories for scvi-tutorials
Users that are interested in scvi-tutorials are comparing it to the libraries listed below
Sorting:
- Spatial reconstruction of dissociated single-cell data☆19Jan 12, 2024Updated 2 years ago
- Template repository for creating novel models with scvi-tools☆20Jan 18, 2023Updated 3 years ago
- Genomic Features in Python from BioConductor's AnnotationHub☆22Feb 23, 2026Updated last week
- Enhancing spatial transcriptomics data by predicting the expression of unmeasured genes from a dissociated scRNA-seq data☆41Jul 1, 2024Updated last year
- Reproducing the experiments of the DestVI paper☆22Feb 9, 2022Updated 4 years ago
- Deep probabilistic analysis of single-cell and spatial omics data☆1,573Updated this week
- Reproducibility for the "Harmonization and Annotation of Single-cell Transcriptomics data with Deep Generative Models" paper☆13Jul 15, 2022Updated 3 years ago
- Single cell perturbation prediction☆335Dec 5, 2024Updated last year
- Reference mapping for single-cell genomics☆399Dec 2, 2025Updated 3 months ago
- Collection of scripts for analysis of pan fetal immune atlas☆29Aug 11, 2022Updated 3 years ago
- ☆13Nov 3, 2023Updated 2 years ago
- ☆11Oct 25, 2022Updated 3 years ago
- Pipeline for the identification of extrachromosomal circular DNA (ecDNA) from Circle-seq, WGS, and ATAC-seq data that were generated from…☆31Jun 3, 2025Updated 9 months ago
- A tool for semi-automatic cell type classification☆453Feb 24, 2026Updated last week
- scOpen: single-cell open chromatin analysis via NMF modelling☆27Feb 4, 2023Updated 3 years ago
- Spatial Single Cell Analysis in Python☆553Updated this week
- identifying disease critical cell types and programs from single cell RNAseq☆58May 30, 2022Updated 3 years ago
- Regulatory network inference and driver gene evaluation using integrative multi-omics analysis and penalized regression☆17Jan 26, 2026Updated last month
- R package for normalisation of spatial transcriptomics data☆17Jan 21, 2026Updated last month
- Spatial-Linked Alignment Tool☆90Dec 20, 2024Updated last year
- Code used to process the data of the HBCA project☆33Feb 9, 2024Updated 2 years ago
- CellRank: dynamics from multi-view single-cell data☆430Updated this week
- A Toolbox for Spatial Transcriptomics Analysis☆166May 6, 2025Updated 9 months ago
- Convert between AnnData and SingleCellExperiment☆144Feb 24, 2026Updated last week
- codes for article☆17Jan 14, 2026Updated last month
- ☆18Sep 13, 2022Updated 3 years ago
- ☆23Sep 29, 2025Updated 5 months ago
- R client for the OmniPath web service☆155Updated this week
- Trans-association between HLA and TCR-CDR3☆19Mar 29, 2023Updated 2 years ago
- Reworked clustering metrics for assessing performance in imbalanced settings☆18Jun 3, 2024Updated last year
- Aligning gene expression trajectories of single-cell reference and query systems☆83Aug 10, 2025Updated 6 months ago
- Automated quantitative analysis of DIA proteomics mass spectrometry measurements.☆21Jan 13, 2025Updated last year
- A tutorial on how to create bioinformatics pipelines as bash scripts, Makefiles and using tools like Nextflow.☆16Nov 14, 2022Updated 3 years ago
- Accelerated, Python-only, single-cell integration benchmarking metrics☆86Feb 24, 2026Updated last week
- scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks☆154Jul 25, 2024Updated last year
- pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which…☆579Jun 26, 2025Updated 8 months ago
- MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological …☆378Oct 3, 2024Updated last year
- Benchmarking analysis of data integration tools☆407Sep 17, 2025Updated 5 months ago
- Single-cell perturbation analysis☆289Feb 23, 2026Updated last week