Does anyone know of an existing software, package, webtool, or suite that can do the full pipeline in one go?
Scan whole genome sequences for user-defined motifs or motifs from public databases
Integrate/enrich with expression sequencing results, including proper normalization
Run k-means clustering on the combined data
Generate heatmaps for visualization
Generate coexpression network plots using and export in cytoscape/related software formats.
I’m looking to benchmark our in-house pipeline against established tools for QC/QA purposes.
I know TB tools-2 can do few of the tasks but still, it's not fully automated. Open to both command-line, standalone app and web-based options. Anything you’ve used and liked.
u/Dismal-Surround-1449 — 26 days ago