{"repo":"immunogenomics/harmony","free":true,"listed":false,"github":"https://github.com/immunogenomics/harmony","clone":"git clone https://github.com/immunogenomics/harmony.git","description":"Fast, sensitive and accurate integration of single-cell data with Harmony","language":"R","stars":667,"topics":["scrna-seq","algorithm","data-integration","r"],"license":null,"category":"data-pipelines","readme_excerpt":"Harmony =========== Integration of large, complex single-cell datasets with Harmony2 Check out our pre-print in biorxiv: - Preprint - Harmony v1 manuscript - package website For Python users, check out the harmonypy package by Kamil Slowikowski. System requirements Harmony has been tested on R versions = 4.2. Please consult the DESCRIPTION file for more details on required R packages. Harmony has been tested on Linux, OS X, and Windows platforms. Installation To install Harmony2, from CRAN (takes approximately 15 seconds): To install Harmony2 from github (development version) from github directly (should take less than 5 minutes): Usage Harmony is designed to be user-friendly and supports some SingleCellExperiment and Seurat R analysis pipelines. Alternatively, it can be used in standalone mode. Quick Start Standalone Mode Check out this vignette for a quick start tutorial which demonstrates the usage of the tool in standalone mode ( 4 seconds). At minimum the following parameters need to be specified to achieve an integration. For a few samples 10M cells) see the OpenMP notes see PERFORMANCE.md our github channel.","default_branch":null,"files":null,"tree":[],"storefront":"/r/immunogenomics","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/immunogenomics/harmony/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."}