Packages
FEATS
FEATS is a new Python tool for performing clustering on single-cell RNA-sequencing data. FEATS can also estimate the number of clusters, perform outlier detection and batch correction and integration of data from multiple experiments. See feats
SingleCell
SingleCell is a Python class available in the singlecelldata package for managing single-cell RNA-seq data. It contains three pandas dataframes; data for holding gene expression values (counts/normalized counts), genedata for holding more information about the genes e.g., gene names, and celldata which contains more information about cells such as cell types, labels etc. See SingleCellData
scplotlib
scplotlib is a python plotting library for the SingleCell object. It is built using Altair. It can generate various plots for data stored in a SingleCell object such as:
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Core plots - line plots, bar plots, scatter plots
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Visualizing high dimensional data - t-SNE plots, PCA plots
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Specialized plots - heatmaps, silhouette plots, outlier score plots
See scplotlib