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,
I've rarely seen worse advice than trying to interpret p-values directly as measures of evidence. This does not work because of Lindley's paradox, and this graph is misleading (a p = 0.04 can be evidence *against* a hypothesis). If you want to talk evidence, use likelihoods. https://t.co/vkALyD4MPy pic.twitter.com/lu8SkC2Zzy
— Daniël Lakens (@lakens) November 17, 2021
I've rarely seen worse advice than trying to interpret p-values directly as measures of evidence. This does not work because of Lindley's paradox, and this graph is misleading (a p = 0.04 can be evidence *against* a hypothesis). If you want to talk evidence, use likelihoods. https://t.co/vkALyD4MPy pic.twitter.com/lu8SkC2Zzy
— Daniël Lakens (@lakens) November 17, 2021This is what happens when someone writes an article on how to "correctly" interpret p-values.
submitted by: Istvan Albert
Can we all agree to google the software names we want to use, to make sure they don't exist already?https://t.co/Yyy7XvQbd8https://t.co/FAZAgNNUvchttps://t.co/R4SDwY788ohttps://t.co/vc41nYSVmn
Also, maybe Bioinformatics (@iscb) could do their own check?
h/t @sialsaffar
— Matthew Hahn (@3rdreviewer) April 14, 2021
Can we all agree to google the software names we want to use, to make sure they don't exist already?https://t.co/Yyy7XvQbd8https://t.co/FAZAgNNUvchttps://t.co/R4SDwY788ohttps://t.co/vc41nYSVmn
Also, maybe Bioinformatics (@iscb) could do their own check?
h/t @sialsaffar
Sounds like CAFE might be a good name to call your next bioinformatics software.
submitted by: Istvan Albert
Fast alignment and preprocessing of chromatin profiles with Chromap | Nature Communications (www.nature.com)
Here we present Chromap, an ultrafast method for aligning and preprocessing high throughput chromatin profiles. Chromap is comparable to BWA-MEM and Bowtie2 in alignment accuracy and is over 10 times faster than traditional workflows on bulk ChIP-seq/Hi-C profiles and than 10x Genomics’ CellRanger v2.0.0 pipeline on single-cell ATAC-seq profiles
submitted by: Istvan Albert
scDeepHash: An automatic cell type annotation and cell retrieval method for large-scale scRNA-seq datasets using neural network-based hashing (www.biorxiv.org)
Automated cell type annotation from scRNA-seq data
submitted by: Mensur Dlakic
RUV-III-NB: Normalization of single cell RNA-seq Data (www.biorxiv.org)
scRNA-seq data normalization
submitted by: Mensur Dlakic
Exhaustively controlling versions of tools and their dependencies as a route to ‘scientific reproducibility’ is a fool's errand.
If your results are meaningful, they will survive the vagaries of different tools and a little numerical instability unmolested. https://t.co/jTWlsz6cW5
— John Marshall (@jomarnz) October 23, 2021
Exhaustively controlling versions of tools and their dependencies as a route to ‘scientific reproducibility’ is a fool's errand.
If your results are meaningful, they will survive the vagaries of different tools and a little numerical instability unmolested. https://t.co/jTWlsz6cW5
submitted by: Istvan Albert
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