Today I learned how to store gene expression data in (multiple) parquet files, and query them as a single dataset from R with the {arrow}, {duckdb} or {sparklyr} packages. I am amazed by {duckdb}'s speed 🚀 - even on my laptop! Here's a blog post with what I learned: https://tomsing1.github.io/blog/posts/parquet/ #TIL #RStats #duckdb #parquet #spark #compbio #rnaseq

Any BLAST users around?

What is this number in the BLAST results? The first number is identity-% and the last is Expect value, but this remains a mystery. It is not the length of the alignment or anything else I can think of...

#blast #question #sequence #alignment #compchem #science #uniprot #compbio

PS: They're hiring! If you're a #computational #scientist interested in #biology #compbio and #genetics, please take a look at open positions like this one for an Associate Computational Scientist ($96,945 - $162,310 DOE):

https://thejacksonlaboratory.wd1.myworkdayjobs.com/en-US/External_JAX/job/Associate-Computational-Scientist_JR003863

They have the coolest data I've ever worked with 🤓

🎙️ NEW #BlackInCompBio PODCAST EPISODE: Navigating Imposter Syndrome with Dr. Javan Carter, Bioinformatics Scientist at @rti_intl. He has had various roles in academia, industry, and now non-profit, and you can tune in to hear about his journey and how we all grappled with talking about imposter syndrome in computational biology. OUT NOW at the link in our bio!

#BlackInCompBio #Podcast #impostersyndrome #CompBio #SciComm #bioinformatics #computationalbiology #science #STEM

🎙️ NEW #BlackInCompBio PODCAST EPISODE: Navigating Imposter Syndrome with Dr. Javan Carter, Bioinformatics Scientist at @rti_intl. He has had various roles in academia, industry, and now non-profit, and you can tune in to hear about his journey and how we all grappled with talking about imposter syndrome in computational biology. OUT NOW at the link in our bio!

#BlackInCompBio #Podcast #impostersyndrome #CompBio #SciComm #bioinformatics #computationalbiology #science #STEM

My day of working in R making plot and finding out that I was behind where I thought I was and many R functions of unexpected default behaviours that still make ZERO sense to me.

#R #bioinformatics #CompBio

Very helpful & thorough assessment of the effect of background counts (ambient RNA, etc) on single-cell RNA-seq analyses: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02978-x #singlecell #compbio #openaccess

RT @saezlab
1/ 📢 New protocol paper for #CellCellCommunication! Our manuscript presents a pipeline for robust and generalizable cell-cell communication analysis of complex single-cell datasets, combining the best of LIANA & Tensor-cell2cell! 💥🔬 #CompBio #SingleCell
https://doi.org/10.1101/2023.04.28.538731

Very cool preprint by Adam P Cribbs's group: "Correcting PCR amplification errors in unique molecular identifiers to generate absolute numbers of sequencing molecules." https://www.biorxiv.org/content/10.1101/2023.04.06.535911v1 with lots of innovative ideas to a) measure and b) correct PCR induced errors in RNA-seq experiments. #rnaseq #ngs #singlecells #compbio #illumina #nanopore

Kicking off the Systems approaches to cancer cell plasticity Symposium at UCL! Looking forward to all the cool talks and posters!
#SACCP #compbio #cancerplasticity #symposium

RT @obenaufa
Lukas is on the job market and he is amazing!

#industry and #academia #wetlab #compbio (within Europe) DM or email me/him if interested pls https://twitter.com/impvienna/status/1629136515677802498

If you are annoyed by connecting and reconnecting Jupyter sessions running on a remote server via SSH tunneling, you might enjoy this command-line tool I made to make this easier: https://github.com/vsbuffalo/remote_jupyter
#compBio

PostDoc Vacancy from Alexandros Stamatakis group to be positioned in Crete.

As I quote from the ad, 'We are looking for computer scientists, Bioinformaticians or "programming Biologists"'

See details in the below link:
https://euraxess.ec.europa.eu/jobs/61879

#bioinformatics #computers #programming #ComputationalBiology #compbio #HPC

:boost_requested:
@jobsecoevo

This direct renin inhibitor ( #aliskiren and #ramiskiren) #compbio study against the Mpro of #sarscov2 is wild
https://pubmed.ncbi.nlm.nih.gov/34514971/

Exciting #NASH story from our #Liver advisor Scott Friedman's lab out in Science Translational Medicine, with @GordianBio playing a small #CompBio role 🎉

Sammi identified new stellate cell behavior to help explain #fibrosis progression, genetic pathways and interventions, 🐭&🧑‍🦰 #singlecell data, paper has it all!

https://www.science.org/doi/10.1126/scitranslmed.add3949

RT @jmuiuc
📢@compbiopitt @PittTweet is searching for a new Chair! Fantastic opportunity to lead a great dept at a top medical school, advance collab with our @CMUCompBio @SCSatCMU, and shape the future of #compbio in #Pittsburgh. Please share within your networks: https://cfopitt.taleo.net/careersection/pitt_faculty_external/jobdetail.ftl?job=22009899

RT @jmuiuc@twitter.com

📢@compbiopitt@twitter.com @PittTweet@twitter.com is searching for a new Chair! Fantastic opportunity to lead a great dept at a top medical school, advance collab with our @CMUCompBio@twitter.com @SCSatCMU@twitter.com, and shape the future of #compbio in #Pittsburgh. Please share within your networks: https://cfopitt.taleo.net/careersection/pitt_faculty_external/jobdetail.ftl?job=22009899

🐦🔗: https://twitter.com/jmuiuc/status/1610354336864821250

Since it’s the new year, I figure an #introduction is in order. My name is Taylor, and I’m entering my final year as a #CompBio PhD candidate at Cornell.
My research is primarily focused on using #ML to understand #regulation of gene expression in grasses. I am particularly interested in #representation and #mechanistic modeling.
My other interests include science in the media, supporting Black scientists, and trivia podcasts.
I hope to have some great discussions on here! :dna: :rna:

Today I learned how to create an interactive HTML report for gene-set enrichment analysis in R. It allows readers to examine set-level results & drill down into the underlying gene-level statistics interactively.
https://tomsing1.github.io/blog/posts/interactive-gene-set-results/
It's a static HTML page, e.g. no server (#shiny, #dash, etc) needed. Thanks a lot to the authors of the #plotly #reactable #crosstalk and #htmlwidget tools for making this so easy #til #rstats #bioconductor #gsea #compbio #visualization @lianos

Happy to get the 100th #citation for our growingly popular 2021 #multiomics review paper!

"State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing": https://www.frontiersin.org/articles/10.3389/fgene.2020.610798/full

Cited by Integrating Rehabilomics into the Multi-Omics Approach in the Management of Multiple Sclerosis: The Way for Precision Medicine? :https://www.mdpi.com/2073-4425/14/1/63

The only challenging side for me it to come to terms with the term "Rehabilomics" ##omics #compbio #metabolomics