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,
#Bioinformatics colleagues! Take a quick look at the top 75 Bioconductor packages.
I discovered some I should've known about but didn't.
The ones I clicked are tied to pathway analysis. pic.twitter.com/TiQoYs6ki7
— Steven Ge (@StevenXGe) June 5, 2023
#Bioinformatics colleagues! Take a quick look at the top 75 Bioconductor packages.
I discovered some I should've known about but didn't.
The ones I clicked are tied to pathway analysis. pic.twitter.com/TiQoYs6ki7
submitted by: Istvan Albert
A survey of mapping algorithms in the long-reads era | Genome Biology | Full Text (genomebiology.biomedcentral.com)
It has been over a decade since the first publication of a method dedicated entirely to mapping long-reads. The distinctive characteristics of long reads resulted in methods moving from the seed-and-extend framework used for short reads to a seed-and-chain framework due to the seed abundance in each read. The main novelties are based on alternative seed constructs or chaining formulations. Dozens of tools now exist, whose heuristics have evolved considerably. We provide an overview of the methods used in long-read mappers. Since they are driven by implementation-specific parameters, we develop an original visualization tool to understand the parameter setting
submitted by: Istvan Albert
Should you always use the Wilcoxon test as a plug-in replacement for the t-test in omics data analysis, because “it makes fewer assumptions” or “it is more robust”? This claim seems to be widely advocated in the bioinformatics world, (1/7)
— Wolfgang Huber 🇺🇦 (@wolfgangkhuber) June 2, 2023
Should you always use the Wilcoxon test as a plug-in replacement for the t-test in omics data analysis, because “it makes fewer assumptions” or “it is more robust”? This claim seems to be widely advocated in the bioinformatics world, (1/7)
— Wolfgang Huber 🇺🇦 (@wolfgangkhuber) June 2, 2023submitted by: Istvan Albert
GitHub - brentp/pbr: drunk on perbase pileups and lua expressions (github.com)
perbase pileups and lua expressions.
submitted by: Istvan Albert
The T2T-CHM13 reference genome has more accurate sequences for immunoglobulin genes than GRCh38 | bioRxiv (www.biorxiv.org)
These studies reveal that the sequences of the immunoglobulin genes within T2T-CHM13 are more accurate than GRCh38. Thus T2T-CHM13 is the reference genome of choice for accurate mapping and identification of the human immunoglobulin genes.
submitted by: Istvan Albert
Data and Code for Reproducible Research: Lessons Learned from the NLM Reproducibility Workshop | Zenodo (zenodo.org)
Goal: Five teams attempted to reproduce bioinformatics papers.
Key takeaway: No papers were successfully reproduced.
submitted by: Istvan Albert
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