The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here.
This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan Albert,
RNA velocity unraveled | bioRxiv (www.biorxiv.org)
We perform a thorough analysis of RNA velocity methods, with a view towards understanding the suitability of the various assumptions underlying popular implementations. In addition to providing a self-contained exposition of the underlying mathematics, we undertake simulations and perform controlled experiments on biological datasets to assess workflow sensitivity to parameter choices and underlying biology. Finally, we argue for a more rigorous approach to RNA velocity, and present a framework for Markovian analysis that points to directions for improvement and mitigation of current problems.
submitted by: Istvan Albert
Benchmarking clustering algorithms on estimating the number of cell types from single-cell RNA-sequencing data | Genome Biology | Full Text (genomebiology.biomedcentral.com)
A key task in single-cell RNA-seq (scRNA-seq) data analysis is to accurately detect the number of cell types in the sample, which can be critical for downstream analyses such as cell type identification. Various scRNA-seq data clustering algorithms have been specifically designed to automatically estimate the number of cell types through optimising the number of clusters in a dataset. The lack of benchmark studies, however, complicates the choice of the methods.
submitted by: Istvan Albert
Curated variation benchmarks for challenging medically relevant autosomal genes | Nature Biotechnology (www.nature.com)
The repetitive nature and complexity of some medically relevant genes poses a challenge for their accurate analysis in a clinical setting. The Genome in a Bottle Consortium has provided variant benchmark sets, but these exclude nearly 400 medically relevant genes due to their repetitiveness or polymorphic complexity. Here, we characterize 273 of these 395 challenging autosomal genes using a haplotype-resolved whole-genome assembly.
submitted by: Istvan Albert
GitHub - jkanche/kana: Single cell RNA-seq analysis in the browser (github.com)
kana is a web application for single-cell RNA-seq data analysis that works directly in the browser. That's right - the calculations are performed client-side, by your browser, on your computer! This differs from the usual paradigm of, e.g., Shiny applications where data needs to be sent to a backend server that does the actual analysis.
submitted by: Istvan Albert
GitHub - cschin/peregrine-2021 (github.com)
Peregrine-2021 is an genome assembler designed for long-reads that have good enough accuracy. It is written with the Rust language. The main method used in the genome assembler is described in Human Genome Assembly in 100 Minutes.
submitted by: Istvan Albert
Want to get the Biostar Herald in your email? Who wouldn't? Sign up righ'ere: toggle subscription
