Researcher in statistics, machine learning and computational biology
Dec 3, 2021 • 14 tweets • 8 min read
Happy to introduce CALDERA, a microbial GWAS method by @hector_rdb extending DBGWAS to better detect polymorphic sequences.
TLDR: we do one test for each closed connected subgraphs of the DBG, where DBGWAS did one per node. Each subgraph can capture several versions of a gene.
De Bruijn graphs (DBGs) connect overlapping k-mers.
Compaction groups simple paths in a single node representing longer subsequences termed unitig.
Local variation (e.g., SNPs) creates bubbles in the graph.
Aug 29, 2019 • 15 tweets • 15 min read
@metapredict The GEO repository did not specify which groups were used for the ROC curves. I offered Dr Timmons to re-run my analysis if he sent me this information but he didn't and when the editor asked him to provide a code reproducing his results, he declined and threatened legal action. @metapredict Most people I told about this answered that it was nonsense as there
was no way such an action could be won. Eventually there was indeed no
action, but I don't think these threats are a nonsense.
@metapredict Most people I told about this answered that it was nonsense as there