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,
The shaky foundations of simulating single-cell RNA sequencing data | Genome Biology | Full Text (genomebiology.biomedcentral.com)
Our results suggest that most simulators are unable to accommodate complex designs without introducing artificial effects, they yield over-optimistic performance of integration and potentially unreliable ranking of clustering methods, and it is generally unknown which summaries are important to ensure effective simulation-based method comparisons.
submitted by: Istvan Albert
Similar story with cancer. Batch correction (not surprisingly) can erase genuine biological differences between batches. By avoiding batch correction, we identified two major colorectal tumour types in scRNA data from 63 patients across 3 countries. https://t.co/MSU6UHEBa2 pic.twitter.com/JA05p4zpvb
— Shyam Prabhakar Lab (@shyam_lab) April 1, 2023
Similar story with cancer. Batch correction (not surprisingly) can erase genuine biological differences between batches. By avoiding batch correction, we identified two major colorectal tumour types in scRNA data from 63 patients across 3 countries. https://t.co/MSU6UHEBa2 pic.twitter.com/JA05p4zpvb
— Shyam Prabhakar Lab (@shyam_lab) April 1, 2023submitted by: Istvan Albert
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor (www.biostars.org)
Mark your calendars for a CCB seminar special with Aaron Lun, the mastermind behind the https://bioconductor.org/books/release/OSCA/ (OSCA) online book!
Aaron will speak about the journey that lead to the OSCA book from a developer's perspective in his talk:
Code, sweat, and tears: how the OSCA sausage was made
When: April 03, 2023, 3 PM ET
Where: https://harvard.zoom.us/j/97173440183?pwd=eHI1ODRub0p5NGNEZncwU0lURlJjdz09
submitted by: Istvan Albert
Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes | BMC Genomics | Full Text (bmcgenomics.biomedcentral.com)
We have analysed several real and mock metagenomes using different methodologies and tools, and compared the resulting taxonomic and functional profiles. Our results show that database completeness (the representation of diverse organisms and taxa in it) is the main factor determining the performance of the methods relying on direct read assignment either by homology, k-mer composition or similarity to marker genes, while methods relying on assembly and assignment of predicted genes are most influenced by metagenomic size, that in turn determines the completeness of the assembly (the percentage of read that were assembled).
submitted by: Istvan Albert
GitHub - tobiasrausch/wally: Wally: Visualization of aligned sequencing reads and contigs (github.com)
Wally:Plotting of aligned sequencing reads, assembled contigs or pan-genome graphs in BAM/CRAM/GFA format and visualization of genomic variants.
submitted by: Istvan Albert
simpleaf: A simple, flexible, and scalable framework for single-cell transcriptomics data processing using alevin-fry | bioRxiv (www.biorxiv.org)
We introduce simpleaf, a program that simplifies the processing of single-cell data using tools from the alevin-fry ecosystem, and adds new functionality and capabilities, while retaining the flexibility and performance of the underlying tools.
submitted by: Istvan Albert
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