{"repo":"Teichlab/cellhint","free":true,"listed":false,"github":"https://github.com/Teichlab/cellhint","clone":"git clone https://github.com/Teichlab/cellhint.git","description":"A tool for semi-automatic cell type harmonization and integration","language":"Python","stars":121,"topics":["cell-type-harmonization","data-integration","machine-learning","python","scrna-seq","single-cell"],"license":"MIT","category":"data-pipelines","readme_excerpt":"CellHint is an automated tool for cell type harmonisation and integration. - harmonisation : match and harmonise cell types defined by independent datasets - integration : integrate cell and cell types with supervision from harmonisation Interactive tutorials Harmonisation Using CellHint for cell type harmonisation Integration Using CellHint for annotation-aware data integration Install CellHint Using pip Using conda Usage (harmonisation) 1. Cross-dataset cell type harmonisation + 1.1. Cell type harmonisation The input AnnData needs two columns in .obs representing dataset origin and cell original annotation respectively. The aim is to harmonise cell types across datasets using cellhint.harmonize. Internally, transcriptional distances between cells and cell types (denoted here as the cell centroid) will first be calculated. Since cell type is usually defined at the cluster level and no cluster is 100% pure, you can set filter cells = True (default to False ) to filter out cells whose gene expression profiles do not correlate most with the cell type they belong to. This will speed up the run as only a subset of cells are used, but will render these filtered cells unannotated (see 2.2. ). Distances are calculated at either gene or low-dimensional space. The latter is preferred to denoise the data by providing a latent representation via the argument use rep (default to PCA coordinates). If X pca is not detected in .obsm and no other latent representations are provided via use r","default_branch":null,"files":null,"tree":[],"storefront":"/r/Teichlab","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/Teichlab/cellhint/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."}