Calling variants in non-diploid systems
The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the se...plished on human mitochondrial DNA although the same approaches will work eq...1038 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.980 days ago
k-mers tutorial - classification and taxonomy
DNA k-mers underlie much of our assembly work, and we (along with many others!) have spent a lo...view 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...977 days ago
Understanding pango networks !
In the vast majority of instances it is expected that Pango lineage names and designat...ineage Designation Committee. https://www.pango.network/the-pango-nomenclature-system...tement-of-nomenclature-rules/ https://www.pango.network/ho...926 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 contact topology in a...s published (1) and reviewed (2); its GNM counterpart is first derived in this work an...834 days ago
Ten quick tips for deep learning in biology
By taking a comprehensive and careful approach to deep learning based on critical thinking about research questions, planning to maintain rigor, and discerning how work mi...766 days ago
CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation
CrowdGO is a protein Gene Ontology predictor using a meta approach, analyzing the predictions of oth...ved precision and recall. Please note that the CrowdGO snakemake workflow is currently only tested on Ubuntu. It should work on...705 days ago
89 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 datasets of protein...g genes. Our goal was to make it straightforward to work from a combination of input s...-quality alignments for phylogenetic inference. The workflo...69 days ago
UniAligner: a parameter-free framework for fast sequence alignment
UniAligner (formerly, TandemAligner) is the first parameter-free algorithm for sequence alignment that introduces...es. Classical alignment approaches, such as the Smith-Waterman algorithm, that work we...52 days ago