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PyWGCNA

PyWGCNA is a python package for preprocessing, analysis, and exploration of bulk RNA sequencing data. This guide is to help developers understand how the PyWGCNA object is structured, how to interact with the object and access data from it, and how to develop new methods for PyWGCNA objects.

Object Overview

The PyWGCNA object is a class allowing for the storage and analysing of bulk data and comparing them to other data types including single-cell and single-nucleus RNA-seq data.

At the top level, the PyWGCNA object serves as a collection of the geneExpr and datExpr objects, representing expression data in an anndata format along with genes and samples information and result of clustering. The geneExpr objects are designed to hold raw expression data of a single type, such as RNA-seq gene expression in anndata format. datExpr objects represent processed expression data along with clustering information. For class-specific details, including a more in-depth description of each variable, please see the wiki sections.