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 Mensur Dlakic, Istvan Albert, and was edited by Istvan Albert,
Single-cell ATAC-seq: strength in numbers | Genome Biology | Full Text (genomebiology.biomedcentral.com)
Single-cell ATAC-seq detects open chromatin in individual cells. Currently data are sparse, but combining information from many single cells can identify determinants of cell-to-cell chromatin variation.
submitted by: Istvan Albert
Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data | bioRxiv (www.biorxiv.org)
Our results demonstrate that ONT variant calls from deep learning-based tools delivered higher SNP and indel accuracy than traditional methods and Illumina, with Clair3 providing the most accurate results overall.
submitted by: Istvan Albert
Improved selection of canonical proteins for reference proteomes | bioRxiv (www.biorxiv.org)
Yet another way to reconcile protein isoforms.
submitted by: Mensur Dlakic
A comparison of marker gene selection methods for single-cell RNA sequencing data | Genome Biology | Full Text (genomebiology.biomedcentral.com)
We compare the performance of the methods using 14 real scRNA-seq datasets and over 170 additional simulated datasets.
Our results highlight the efficacy of simple methods, especially the Wilcoxon rank-sum test, Student’s t-test, and logistic regression.
submitted by: Istvan Albert
https://academic.oup.com/bioinformaticsadvances/advance-article/doi/10.1093/bioadv/vbae031/7616126?login=false
We introduce trackplot, a minimal R script designed for the rapid generation of integrative genomics viewer (IGV) style track plots, profile plots, and heatmaps from bigWig files. This script offers speed, owing to its reliance on bwtool, resulting in performance gains of several magnitudes compared to equivalent packages. The script is lightweight, requiring only the data.table and bwtool packages as primary dependencies. Notably, the plots are generated in base R graphics, eliminating the need for additional packages.
submitted by: Istvan Albert
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