EpiScanpy is a toolkit to analyse single-cell open chromatin (scATAC-seq) and single-cell DNA methylation (for example scBS-seq) data. EpiScanpy is the epigenomic extension of the very popular ...
An implementation of MNN correct in python featuring low memory usage, full multicore support and compatibility with the scanpy framework. Batch effect correction by matching mutual nearest neighbors ...
Spatially resolved transcriptomics (SRT) technologies, such as spatial transcriptomics (ST) (Ståhl et al., 2016), 10x Visium, and Slide-seqV2 (Stickels et al., 2021), can measure the transcript ...
The input data is preprocessed with the Scanpy package in Python. Starting from the raw gene-cell count matrix, library size normalization is performed to scale the total counts of each cell to be ...
SCANPY is a scalable toolkit for analyzing single-cell gene expression data. It includes methods for preprocessing, visualization, clustering, pseudotime and trajectory inference, differential ...
Tumor heterogeneity is widely attributed to the imperfection of DNA replication. However, little is known about the mechanoregulation of tumor heterogeneity. Here, we report that volumetric ...
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