Disease Association Protein-Protein Link Evaluator (Broad hosted algorithm)
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Updated
Jan 3, 2024 - Python
Disease Association Protein-Protein Link Evaluator (Broad hosted algorithm)
This is basic GenePattern module written in Python 3. It can be taken as a Template for future modules. (click 'Use this template' to get started)
Wraps the AmpliconSuite-pipeline workflow to identify one or more connected genomic regions which have copy number amplifications.
Actual creation of the Elastic Principa Graph in the STREAM scRNASeq Trajectory analysis, packaged as a GenePattern module
Detect differentially expressed genes between pairs of trajectory branches
Repo for the HISAT2 .ndexer module which creates indices for the HISAT2.aligner module
Detect marker genes that distinguish the different trajectories
Generate the signature subway and stream plots
Step one of the STREAM ssRNA-Seq Trajectory pipeline
scVelo wrapper module for GenePattern
This module will turn a TXT file into ComparativeMarkerSelectionViewer-compatible ODF file
STREAM can be used to detect cell population-specific markers. This is similar to leaf branch marker gene detection. Here instead of comparing the gene expression values between leaf branches, we compare the gene expression values between cell populations
Detect transition genes for each branch of the trajectory.
Repo for the dockerized HISAT2.aligner module
An optional final step to optimize branching, prune the graph or extend leaf nodes following generation of the Elastic Principal Graph
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