theislab / scib-pipeline
Snakemake pipeline that works with the scIB package to benchmark data integration methods.
☆68Updated last month
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.☆64Updated this week
- R package for semi-supervised single-cell data integration☆79Updated last year
- Analysis of cell-cell communication at single-cell resolution☆100Updated 6 months ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆59Updated 9 months ago
- Code repository for the Tumor Immune Cell Atlas (TICA) project☆62Updated 2 years ago
- Efficient and precise single-cell reference atlas mapping with Symphony☆103Updated 2 years ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆59Updated 6 months ago
- Single cell omics biology annotations☆50Updated this week
- ☆46Updated 2 years ago
- R package for pathway analysis in scRNA-seq data☆70Updated 6 months ago
- Methods to compute Local Inverse Simpson's Index (LISI)☆61Updated 3 years ago
- Python package for analysis of multiomic single cell RNA-seq and ATAC-seq.☆61Updated 10 months ago
- Python implementation of Milo for differential abundance testing on KNN graph☆63Updated 3 weeks ago
- marker-based purification of cell types from single-cell RNA-seq datasets☆106Updated last month
- Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.☆93Updated last year
- A python-based package and software to predict metabolite mediated cell-cell communications by single-cell RNA-seq data☆71Updated 3 months ago
- Coarse-graining of large single-cell RNA-seq data into metacells☆73Updated 6 months ago
- A repository of pipelines for single-cell data in Nextflow DSL2☆75Updated last year
- Gene regulatory network containing signed transcription factor-target gene interactions☆71Updated 10 months ago
- Functional Inference of Gene Regulation☆40Updated 8 months ago
- ☆59Updated 5 years ago
- Niche Interactions and Cellular Heterogeneity in Extracellular Signaling☆51Updated 5 months ago
- ☆49Updated 5 months ago
- This repository contains all code used for the Human Lung Cell Atlas project.☆49Updated last year
- inferring cell-cell communication from scRNA-seq of ligand-receptor☆78Updated last year
- Framework for sensitive DE testing (using neighbourhoods)☆64Updated 7 months ago
- Code to reproduce the analysis of "Decoding gene regulation in the mouse embryo using single-cell multi-omics""☆40Updated 2 years ago
- DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map th…☆109Updated last year
- Methods to discover gene programs on single-cell data☆104Updated last week
- trajectory inference☆96Updated last month