{"repo":"sanderlab/scPerturb","free":true,"listed":false,"github":"https://github.com/sanderlab/scPerturb","clone":"git clone https://github.com/sanderlab/scPerturb.git","description":"scPerturb: A resource and a python/R tool for single-cell perturbation data","language":"Jupyter Notebook","stars":182,"topics":["cite-seq","database","perturbation","scatac-seq","science","scrna-seq","single-cell","python","r","statistics"],"license":null,"category":"databases-storage","readme_excerpt":"scPerturb: A resource and a python tool for single-cell perturbation data For the publication see: Peidli, S., Green, T.D., et al. Nature Methods (2024). Where to find the data The datasets are available to download on scperturb.org (where you can also find an interactive table of all included datasets). The latest versions are available in full on Zenodo, depending on the modality you are interested in: - RNA data - ATAC data Most datasets are also downloadable via pertpy or Lamin. scperturb for python (integrates with scanpy) A python package to compute E-distances in single-cell perturbation data and perform E-tests. Please note that maintenance on the scperturb Python package is relatively slow. We have recreated Python functionality in pertpy which has a larger base of support and also includes fast calculation of alternative distance metrics and tests. Install Just install via pip: Usage example Check out this notebook for a tutorial. Basic usage is: scperturbR for R (integrates with Seurat) We wrote an R version of scperturb that works with Seurat objects. You can find it as scperturbR on CRAN. A basic usage vignette is WIP. Install using: Reproducibility Instructions to run the code to reproduce the figures and tables in the paper and supplement: - install conda if necessary (also check out mamba, it's way faster) - run \"conda env create -f sc env.yaml\" to create a new conda environment with all the necessary packages to run the code ( you will need this ) - activate ","default_branch":null,"files":null,"tree":[],"storefront":"/r/sanderlab","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/sanderlab/scPerturb/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}