parashardhapola / scarfLinks
Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.
☆100Updated 2 months ago
Alternatives and similar repositories for scarf
Users that are interested in scarf are comparing it to the libraries listed below
Sorting:
- Convert between AnnData and SingleCellExperiment☆137Updated this week
- Doublet detection in single-cell RNA-seq data.☆91Updated 5 months ago
- ☆130Updated last year
- Single-Cell Clustering Assessment Framework☆103Updated last year
- ☆44Updated last week
- A tool that allows to get UMI counts from a single cell protein assay☆82Updated 2 months ago
- Python implementation of Milo for differential abundance testing on KNN graph☆72Updated 4 months ago
- Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…☆150Updated last month
- A repository of pipelines for single-cell data in Nextflow DSL2☆75Updated 2 years ago
- Context specific and dynamic gene regulatory network reconstruction and analysis☆119Updated this week
- software to detect doublets☆93Updated 6 months ago
- ☆55Updated last month
- Geometry-preserving random sampling☆87Updated 8 months ago
- Scanpy use cases.☆85Updated 4 years ago
- A docker image for single-cell analysis☆88Updated 5 months ago
- trajectory inference☆104Updated 5 months ago
- Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cel…☆64Updated last year
- A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA seq…☆63Updated 2 weeks ago
- Snakemake pipeline that works with the scIB package to benchmark data integration methods.☆74Updated 5 months ago
- Cluster single cells and analyze cell clade relationships with colorful visualizations.☆114Updated 8 months ago
- User-friendly tool to infer cell-cell interactions and communication from gene expression of interacting proteins☆61Updated last week
- Metacells - Single-cell RNA Sequencing Analysis☆108Updated 9 months ago
- Filtering of Poison noise on a single-cell RNA-seq UMI count matrix☆77Updated 2 months ago
- dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data☆117Updated this week
- Tools for single-cell data processing☆125Updated last year
- Clonotype Neighbor Graph Analysis☆89Updated 3 weeks ago
- Inference of RNA velocity modules for prediction of cell fates and integration with spatial and regulatory models.☆77Updated 3 months ago
- R package to access DoRothEA's regulons☆149Updated last year
- pycisTopic is a Python module to simultaneously identify cell states and cis-regulatory topics from single cell epigenomics data.☆68Updated this week
- ☆47Updated 3 years ago