{"repo":"cbib/Seurat-Integrate","free":true,"listed":false,"github":"https://github.com/cbib/Seurat-Integrate","clone":"git clone https://github.com/cbib/Seurat-Integrate.git","description":"R package expanding integrative analysis capabilities of Seurat by providing seamless access to popular integration methods and to an integration benchmarking toolkit.","language":"R","stars":35,"topics":["batch-effects","data-integration","scrna-seq","seurat","single-cell-genomics","single-cell-rna-seq"],"license":null,"category":"data-pipelines","readme_excerpt":"SeuratIntegrate R package expanding integrative analysis capabilities of Seurat by providing seamless access to popular integration methods. It also implements an integration benchmarking toolkit that gathers well-established performance metrics to help select the most appropriate integration. Examples, documentation, memos, etc. are available on the SeuratIntegrate's website. SeuratIntegrate provides support to R- and Python-based integration methods. The table below summarizes which methods are compatible with SeuratIntegrate: Table 1: Supported integration methods Package Method Function R SeuratIntegrate ComBat CombatIntegration() Harmony HarmonyIntegration() MNN MNNIntegration() Seurat CCA CCAIntegration() RPCA RPCAIntegration() SeuratWrappers FastMNN ( batchelor ) FastMNNIntegration() Python SeuratIntegrate BBKNN bbknnIntegration() scVI scVIIntegration() scANVI scANVIIntegration() Scanorama ScanoramaIntegration() trVAE trVAEIntegration() - Installation - Preparations - Setup Python environments - Setup a SeuratObject - Facultative dependencies - SeuratIntegrate usage - Integrate datasets - Post-process integration outputs - Compare integrations - Getting help and advice - Citing Installation First, use the yaml files to creates environments using conda https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html Install SeuratIntegrate from github directly: Preparations Setup Python environments To use Python methods, run the following commands (once) to","default_branch":null,"files":null,"tree":[],"storefront":"/r/cbib","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/cbib/Seurat-Integrate/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."}