Spycone - SPlicing-aware time-COurse Network Enricher

Spycone is a python package that provides systematic analysis of time course transcriptomics data. It uses gene or isoform expression and a biological network as an input. It employs the sum of changes of all isoforms relative abundances (total isoform usage) across time points to detect IS events. Spycone further provides downstream analysis such as clustering by total isoform usage, gene set enrichment analysis, network enrichment, and splicing factors analysis. Below we describe the Spycone workflow in detail. .

Installation

Prerequisite

Spycone is dependent on the pcst_fast library, which is not available through pip install. Please go to the github page or run this command.:

pip install https://github.com/fraenkel-lab/pcst_fast/archive/refs/tags/1.0.7.tar.gz

To install Spycone:

pip install spycone

To install the latest development:

git clone https://github.com/yollct/spycone.git
cd spycone
pip install .

Contents

• Gene-level workflow
  • Prepare the dataset
  • Preprocessing
  • Clustering
  • Gene set enrichment analysis
  • Run DOMINO
• Transcript-level workflow
  • Prepare the dataset
  • Preprocessing
  • Detect isoform switch
  • Clustering of total isoform usage
  • Gene set enrichment analysis
  • DOMINO on the domain level
  • Splicing Factor analysis
• API
  • Import dataset
  • Import and store biological network
  • Preprocessing
  • Isoform-level function
  • Perfom clustering
  • GO terms enrichment analysis
  • Run DOMINO
  • Visualization
  • Splicing factor analysis

• Search Page