jfy133.genomic.social.ap.brid.gy
James Fellows Yates
@jfy133.genomic.social.ap.brid.gy
6 followers 0 following 5 posts
Bioinformatician in #Metagenomics, #Palaeogenomics / #aDNA, #Microbiomes. Loving #nextflow and #OpenScience. @MPI_EVA_Leipzig / @LeibnizHKI. Core team member of […] 🌉 bridged from ⁂ https://genomic.social/@jfy133, follow @ap.brid.gy to interact
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jfy133.genomic.social.ap.brid.gy
James Fellows Yates @jfy133.genomic.social.ap.brid.gy · 29d
Do you work in #bioinformatics, love #conda & #bioconda, but didn't know how to start adding (or debugging) your/someone else's software to it?

Here's a three-part (opinionated) guide for the #microbifinie blog on just that, based on my own experiences!

Adding […]
Original post on genomic.social
genomic.social
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jfy133.genomic.social.ap.brid.gy
James Fellows Yates @jfy133.genomic.social.ap.brid.gy · 16h
Do you perform analysis on #metagenomics, #metataxonomics #metatranscriptomics #metaproteomics datasets?

Would you like to find out how to make your #bioinformatic analysis more efficient, scalable, and reproducible?

Join us on December 10th for an online […]

[Original post on genomic.social]
Poster advertising an event Meta-*omics Nextflow Pipeline Community Exhibition Day Do you work with . Want to find out how to metagenomics, metaxaxonomics, make your analysis more metaproteomics, metatranscriptomics efficient, scalable, and datasets? reproducible? Meet developers for an introduction and practical hands-on demonstration of their meta-*omics Nextflow pipelines! When is it happening? December 10th 2026. Times pending Where is happening? Online! Platform pending What do you need? - Ability to navigate the UNIX command line Online - Be already familiar with basic theory/concepts pjatform pending of the analysis of your meta-*omics data - A computer, and an internet connection Interested? Register your interest and choose your pipeline(s) https://tally.so/r/31gJyQ Supported by NFDI4MIcrobiota and NextflowAmbassadors Poster advertising event Featured pipelines nf-core/createtaxdb (nf-co.re/createtaxdb) nf-core/createtaxdb is a bioinformatics pipeline that constructs custom metagenomic classifier databases for multiple classifiers and profilers from the same input FASTA reference genome set in a highly automated and parallelised manner. Biobakery-nextflow (github.com/BonhamLab/biobakery-nextflow) Shotgun metagenomics community profiling (taxonomic and functional) of Illumina short read data using the Biobakery suite of tools and databases. epi2me-labs/wf-metagenomics (github.com/epi2me-labs/wf-metagenomics) Taxonomic classification of Nanopore sequenced metagenomic sequencing data and identification of antimicrobial resistance (AMR) or virulence genes. It includes an optional step to remove host sequences. It can also be run through the EPI2ME Desktop Application. nf-core/taxprofiler (nf-co.re/taxprofiler) nf-core/taxprofiler is a pipeline for taxonomic classification and profiling of shotgun short- and long-read metagenomic data. It performs in-parallel taxonomic identification of reads or taxonomic abundance estimation with multiple classification and profiling tools against multiple databases, with standardised output profiles. (and more! Please contact James Fellows Yates for the rest of the list - hitting Alt text limits now)
jfy133.genomic.social.ap.brid.gy
James Fellows Yates @jfy133.genomic.social.ap.brid.gy · 1d
🎁 Another week, another pipeline release!

🚀 This week it's the latest version of @nf_core 's funcscan , assembled contigs and genomes for functional genes.

🥐 v3.0.0 French Chocolatine (in honour of @gau ), with major tool version upgrades for antiSMASH (for […]

[Original post on genomic.social]
Pipeline diagram in the style of a london underground map for nf-core funcscan. There are three sections 1 for preprocessing, 2 for functional contig screening of ARG, AMP, and BGC with different tools, and finally results aggregation for summary outputs.
Reposted by James Fellows Yates
astroroyalscot.bsky.social
Astronomer Royal for Scotland | Catherine Heymans @astroroyalscot.bsky.social · 4d
Conventional wisdom says motherhood should wait for tenure as before you land a permanent post, #academia is just not that family friendly🙁

@carersinstemm.bsky.social are calling for change and to celebrate their new report, a Saturday🧵on parenting & academia! 1/9 👩‍🔬🧪🔭⚛️

ℹ️: carersinstemm.co.uk
From 2006. A younger and shell-shocked looking Catherine on a balcony holding a very tiny baby with the mountains of Vancouver in the background. The baby is so new, Catherine still has the pregnant bump.
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Reposted by James Fellows Yates
ropensci.org
rOpenSci @ropensci.org · 6d
🎙️ Resources from Community Call "R-multiverse: a new way to publish R packages" with @landau

✅ video with subtitles
✅ R-multiverse website with guidelines to participate in
✅ collaborative notes

https://ropensci.org/commcalls/r-multiverse/

#rstats @RConsortium
R-multiverse: a new way to publish R packages · Community Call
Community Call about R-multiverse
ropensci.org
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Reposted by James Fellows Yates
potterybyosa.mastodon.social.ap.brid.gy
Pottery by Osa @potterybyosa.mastodon.social.ap.brid.gy · 6d
I usually make things for people to use at home, but it seems to me that the only purpose of this bowl is to bob and spin in the Gulf.

#ceramics #pottery #nature #water #beach #florida #birds #PeacefulMoments
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Reposted by James Fellows Yates
opencontext.hcommons.social.ap.brid.gy
Open Context @opencontext.hcommons.social.ap.brid.gy · 13d
Paulina Przystupa is bringing #archaeology #dataliteracy instructional materials to the #oer commons!

Here's an example of free teaching materials for you to adapt and reuse:

https://oercommons.org/courses/cow-culating-your-data-with-spreadsheets-and-r

Many more such resources are on their […]
Original post on hcommons.social
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jfy133.genomic.social.ap.brid.gy
James Fellows Yates @jfy133.genomic.social.ap.brid.gy · 13d
📣 Last call 📣

👨🏾‍💻 Do you develop a #nextflow #pipeline for #metagenomics, #metataxonomics, #metatranscriptomics, #metaproteomics

🎉 Represent your pipeline at an upcoming community 'meta-omics' exhibition day by giving a tutorial!

✏️ Register your interest to demo your pipeline […]
Original post on genomic.social
genomic.social
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Reposted by James Fellows Yates
b0rk.social.jvns.ca.ap.brid.gy
Julia Evans @b0rk.social.jvns.ca.ap.brid.gy · 22d
where this came from is that I made a Git cheat sheet a while back at https://wizardzines.com/git-cheat-sheet.pdf

and then I found out that the folks who make the official Git website are super open to contributions and thought "... wait, the website doesn't have a cheat sheet, I could just […]
Original post on social.jvns.ca
social.jvns.ca
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Reposted by James Fellows Yates
b0rk.social.jvns.ca.ap.brid.gy
Julia Evans @b0rk.social.jvns.ca.ap.brid.gy · 22d
added a cheat sheet to the official Git website https://git-scm.com/cheat-sheet
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jfy133.genomic.social.ap.brid.gy
James Fellows Yates @jfy133.genomic.social.ap.brid.gy · 23d
❓ Do you develop a #nextflow pipeline for #metagenomics, #metataxonomics, #metatranscriptomics, #metaproteomics, etc?

🧑‍💻 I'm looking for #bioinformatics developers to give demos of their #opensource pipelines to the scientific community in a ‘Meta-*omics Nextflow pipeline community exhibition […]
Original post on genomic.social
genomic.social
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jfy133.genomic.social.ap.brid.gy
James Fellows Yates @jfy133.genomic.social.ap.brid.gy · 29d
Do you work in #bioinformatics, love #conda & #bioconda, but didn't know how to start adding (or debugging) your/someone else's software to it?

Here's a three-part (opinionated) guide for the #microbifinie blog on just that, based on my own experiences!

Adding […]
Original post on genomic.social
genomic.social
1