TrendBio

#5 · Tools & infrastructure

Packaged software integrates capture probe and oligo pool library design workflows

4 preprints · 4 published · ↑ 2.2× vs 4-wk avg
Items per day, last 8 weekstoday: 8

The dominant thread is computational design of nucleic acid reagents delivered as installable software. BaitBench, written in Rust, combines hybrid capture probe design, assessment and thermodynamic simulation behind both CLI and GUI interfaces, and reports a correlation of rho=0.916 in its outcome prediction. PoolParty represents oligo pool DNA libraries as computational graphs, exposing more than 50 mutagenesis, motif and barcode operations and generating design cards. The shared contribution is consolidating design and, for BaitBench, in silico evaluation into one package rather than separate stages. The remaining items are packaged analysis infrastructure for other problems: rare-variant aggregation across genes and pathways (DoAggregate, 36 methods), ABCD/HBCD dataset construction (NBDC Data Tools), single-cell count generation and per-cell QC (gcat, its_a_scam), single-sample regulatory networks (SiSaNA), matched Ribo-seq/RNA-seq profiling (Ribotools), and a static-file reimplementation of dictyBase. These share the packaging emphasis but not the reagent design focus.

Published papers

Preprints

Topic history

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