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1. TEA-GCN TEA-GCN Public

   The TEA-GCN pipeline to construct gene co-functional and co-regulatory networks from public transcriptomes using condition-specific ensemble co-expression. Refer to our paper published in Nature Co…

   Python 22 4

2. LSTrAP-denovo LSTrAP-denovo Public

   LSTrAP-denovo is an easy-to-use pipeline to assemble and annotate transcripts for species without genome / genomic annotations using publicly available RNA-seq data.

   Python 6 3

3. CxNE_plants CxNE_plants Public

   Generation Co-expression Network Embeddings (CxNEs) for plant genes using Graph Attention Networks (GAT))

   Python 2 1

4. epidemiological-overlap epidemiological-overlap Public

   Scripts to contextualize AMR transmission linkages between Enterobacterales isolates with patient metadata and related analyses. Current version is based on methods from https://doi.org/10.1038/s41…

   Python 1

5. ViralGenomeEpi ViralGenomeEpi Public

   End-to-end Clinical mNGS pipeline for de novo viral genome assembly, phylogenetics, and epidemiological cluster tracking.

   Python 1

6. ONTEnsembleAMR ONTEnsembleAMR Public

   [UNDER DEVELOPMENT] Repo to detect AMR resistance from Metagenome ONT reads using multiple state-of-the-art AMR detection tools