Calling variants in non-diploid systems
...variants. Some of the early attempts to do this well have been accomplished on human mitochondrial DNA although the same approaches will work equally good on viral and bac...1040 days ago
RNA-Seq differential expression work flow using DESeq2
One of the aim of RNAseq data analysis is the detection of differentially expressed genes. The package DESeq2 provides methods to test for differential expression analysis.983 days ago
k-mers tutorial - classification and taxonomy
DNA k-mers underlie much of our assembly work, and we (along with many others!) ha...ew and waxing enthusiastic about other people's work. Then in a future blog post I'll talk about how we're building off of this work in fun! and interesting? ways...980 days ago
Understanding pango networks !
...cisions made by the Lineage Designation Committee. https://www.pango.network/the-pango-nomenclature-system/statement-of-nomenclature-rules/ https://www.pango.network/how-does-the-system-work/what...929 days ago
oGNM:Conformational dynamics based on contact topology in a coarse-grained presentation
Gaussian Network Model (GNM) is a powerful tool to sample conformational dynamics based on co...published (1) and reviewed (2); its GNM counterpart is first derived in this work and proven to be more accurat...836 days ago
Ten quick tips for deep learning in biology
...rehensive and careful approach to deep learning based on critical thinking about research questions, planning to maintain rigor, and discerning how work might have far-reaching conse...768 days ago
CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation
...he predictions of other tools in order to get an improved precision and recall. Please note that the CrowdGO snakemake workflow is currently only tested on Ubuntu. It should work on OSX, but please report any...707 days ago
91 days ago
Orthoflow: workflow for phylogenetic inference of genome-scale datasets of protein-coding genes
Orthoflow is a workflow for phylogenetic inference of genome-scale da...genes. Our goal was to make it straightforward to work from a combination of input s...uality alignments for phylogenetic inference. The workflow produces a detailed repor...71 days ago
UniAligner: a parameter-free framework for fast sequence alignment
...t scoring that automatically changes for any pair of compared sequences. Classical alignment approaches, such as the Smith-Waterman algorithm, that work well for most sequences, fail...54 days ago