Many RNAseq experiments are designed around explicit biological logic: genotype, treatment, rescue, sex, time, injury, or combinations of these variables.
LCS — Logical Clustering Suite — was developed to organize differential expression results around those experimental relationships. (2/5)
Rather than clustering genes only by global similarity, LCS asks whether genes satisfy defined logical patterns across contrasts.
Examples include: mutant-specific changes, treatment-rescued genes, shared injury responses, sex-dependent effects, or signatures excluded from control conditions. (3/5)
Wow, porting to C++ took only an hour and made the app a trillion times faster...shocking....should have done this earlier.
I am (well...AI is) currently porting LCS 3.0 from MATLAB to C++ to compile it into binaries that can be used by standard bio-info pipelines. Stick around...
This can be useful when the main biological question is conditional rather than purely unsupervised.
LCS is intended to complement established RNAseq workflows such as edgeR/R analysis by adding an interpretable layer for grouping and comparing gene signatures. (4/5)
Fintastic lay summary by @unevadareno.bsky.social on recent #cavefish work from the Riddle Lab 🐟
🔗 to original research published in @currentbiology.bsky.social: www.cell.com/current-biol...
Now live: LCS 3.0 engine rebuild with C++ with command line our GUI interface. Optional bioconductor edgeR filters and stats (slow), and fast internal stats (correlationdistance & welch test). Can be integrated into any bioinformatics pipline as executable. (1/5)🧵 zenodo.org/records/2063...
The goal is not to replace classical clustering, PCA, or differential expression testing, but to make complex experimental designs easier to query, document, integrate, and communicate. (5/5) Concept published in:
www.cell.com/cell-reports...
Smile like Megalochelys atlas because it’s #FossilFriday! This species was one of the largest known land turtles & lived during the Late Pliocene ~2 million years ago. This specimen’s shell measures some 7.4 ft (2.3 m) long and in life, it may have weighed more than 2,000 lbs (907 kg)!
