theislab / scib-pipeline
Snakemake pipeline that works with the scIB package to benchmark data integration methods.
☆71Updated 3 months ago
Alternatives and similar repositories for scib-pipeline:
Users that are interested in scib-pipeline are comparing it to the libraries listed below
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆68Updated 3 weeks ago
- Analysis of cell-cell communication at single-cell resolution☆100Updated 7 months ago
- Code repository for the Tumor Immune Cell Atlas (TICA) project☆61Updated 3 years ago
- R package for semi-supervised single-cell data integration☆81Updated last month
- R package for pathway analysis in scRNA-seq data☆73Updated 8 months ago
- marker-based purification of cell types from single-cell RNA-seq datasets☆110Updated last week
- ☆46Updated 2 years ago
- Python implementation of Milo for differential abundance testing on KNN graph☆68Updated 2 months ago
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆61Updated last year
- Efficient and precise single-cell reference atlas mapping with Symphony☆104Updated 2 years ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆60Updated 10 months ago
- Methods to compute Local Inverse Simpson's Index (LISI)☆61Updated 3 years ago
- Single cell omics biology annotations☆51Updated 2 weeks ago
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆52Updated last week
- R/MATLAB package to perform virtual knockout experiments on single-cell gene regulatory networks.☆45Updated 4 months ago
- Functional Inference of Gene Regulation☆43Updated 10 months ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆73Updated last month
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Updated 2 years ago
- A repository of pipelines for single-cell data in Nextflow DSL2☆75Updated 2 years ago
- Capybara: A computational tool to measure cell identity and fate transitions☆58Updated 2 years ago
- Collection of Tumor-Infiltrating Lymphocyte Single-Cell Experiments with TCR☆84Updated 10 months ago
- trajectory inference☆97Updated 3 months ago
- Single Cell Transcriptomics of 25 Human Organs to Create a Tabula Sapiens☆41Updated last year
- Coarse-graining of large single-cell RNA-seq data into metacells☆77Updated 8 months ago
- Pan-Cancer Single Cell Classifier☆68Updated 11 months ago
- Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.☆94Updated last year
- ☆50Updated 7 months ago
- Single-cell Lung Cancer Atlas with 1.2M cells☆62Updated 3 months ago
- Create cisTarget databases☆50Updated 3 months ago
- Principal analysis code used in for analysis of single cell RNAseq of primary untreated colon cancer. As described in: "Spatially organiz…☆39Updated 3 years ago