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 zx8754, Istvan Albert, and was edited by Istvan Albert,
RGC - Public Variant Browser (rgc-mcps.regeneron.com)
About MCPS Variant Browser This variant browser summarizes the genetic variation observed in 9,950 whole genome sequenced and 141,046 exome sequenced and genotyped individuals from the Mexico City Prospective Study (MCPS). This includes genome locations, population specific allele frequencies, alleles and annotations for 142 million variants.
submitted by: zx8754
CSDL | IEEE Computer Society (www.computer.org)
We have been trying to get software engineering researchers and practitioners to talk to one another for over a decade. This paper describes what we have done, assesses our impact, and recommends an approach that we hope will have greater success.
submitted by: Istvan Albert
Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies | Genome Biology | Full Text (genomebiology.biomedcentral.com)
Here, we propose k-mer based and 16S RNA based methods to measure the completeness of metagenome assembly. We show that even with PacBio high-fidelity (HiFi) reads, abundant species are often not assembled, as high strain diversity may lead to fragmented contigs.
submitted by: Istvan Albert
RummaGEO (rummageo.com)
Rummage through 135,264 human and 158,062 mouse gene sets automatically generated by computing signatures from 23,395 GEO studies to find the most similar gene sets that match your query.
submitted by: Istvan Albert
RummaGEO: Automatic Mining of Human and Mouse Gene Sets from GEO | bioRxiv (www.biorxiv.org)
We developed RummaGEO, a webserver application that enables gene expression signature search of a large collection of human and mouse RNA-seq studies deposited into GEO
submitted by: Istvan Albert
Modern Data Visualization with R (rkabacoff.github.io)
This is the online version of “Modern Data Visualization with R”, published by CRC Press.
submitted by: Istvan Albert
Where did BWA come from? (lh3.github.io)
submitted by: Istvan Albert
New Sniffles (SV caller for @PacBio & @nanopore ) version public https://t.co/laDSuLEoVN . . Improvements on sample merging & smaller issues. Going forward more consistent releases to come and thanks everyone for reporting issues! @lfpaulin @BCM_HGSC @bcmhouston @RiceCompSci
— Fritz Sedlazeck (@sedlazeck) April 11, 2024
New Sniffles (SV caller for @PacBio & @nanopore ) version public https://t.co/laDSuLEoVN . . Improvements on sample merging & smaller issues. Going forward more consistent releases to come and thanks everyone for reporting issues! @lfpaulin @BCM_HGSC @bcmhouston @RiceCompSci
— Fritz Sedlazeck (@sedlazeck) April 11, 2024submitted by: Istvan Albert
Analyses of 600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges (genome.cshlp.org)
We investigated REs across 601 insect species and report wide variation in RE dynamics across groups. Analysis of associations between REs and protein-coding genes revealed dynamic evolution at the interface between REs and coding regions across insects, including notably elevated RE–gene associations in lineages with abundant long interspersed nuclear elements (LINEs).
submitted by: Istvan Albert
GitHub - CompEpigen/figeno: Tool for making genomics figures (github.com)
Tool for making genomics figures.
submitted by: Istvan Albert
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