PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

Automated machine learning for analyzing, interpreting, and designing biological sequences

Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space

A Python library to visualize and analyze long-read transcriptomes

Code to calculate the Splicing Z Score (SpliZ) for single cell RNA-seq splicing analysis

Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.

Interpretable splicing model

Leaflet is a probabilistic model that identifies latent cell states defined by splicing changes.

A Cloud Pipeline to Analyze Long Read Sequencing Data from Oxford Nanopore and PacBio Sequencers

Applying network-level analysis to the RNA-seq data from The Cancer Genome Atlas pan-cancer dataset

Module Alignment of TranscripTomE analysis

NEASE tutorials

tool for long read transcriptome assembly