Calling variants in non-diploid systems
The main challenge associated with non-diploid variant calling is the difficulty in distinguishing between the sequencing noise (abundant in all NGS platforms) and true low...1057 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.1000 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 lot of time thinking about how to store k-mer graphs efficiently, dis...997 days ago
Understanding pango networks !
In the vast majority of instances it is expected that Pango lineage names and designations will conform to the following rules. These rules also act as guidelines for the d...945 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 coarse-grained presentation. Here we present a method to co...853 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 mig...785 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 other tools in order to get an improved precision and recall. Please note...724 days ago
108 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-coding genes. Our goal was to make it straightforward to work from a combination of i...88 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 a sequence-dependent alignment scoring that automatically...71 days ago