lieven clement

[lieven clement @lievenClement]

Our new e-course on statistics for MS-based proteomics data analysis is now online. Learn the basics and how to document your analyses in fully reproducible reports using R/RStudio or our shinyApp: https://t.co/CLTuUO66Uc

[Jeroen Gilis @GilisJeroen]

Why would we only care about differences in the **average** gene expression in a scRNA-seq DE analysis? 🤔

We present a framework to jointly test for differences in average gene expression and gene DETECTION. Extra hypothesis tested, no extra cost!

https://t.co/1V7EKNswyk

[Rafael Irizarry @rafalab]

Clustering algorithms report clusters even when none exist. In single-cell RNA-Seq pipelines, novel cell types are often identified by clustering algorithms. Expanding on Kimes et al.'s work, we introduce significance analysis for single-cell RNA-Seq data: https://t.co/ut1kPjKVCM

[lieven clement @lievenClement]

Fast differential usage, aberrant splicing and expression analysis that scales to large RNA-seq data compendia? Check @Alex_Segers_ preprint to see how juggling offsets unlocks bulk RNA-seq tools for these applications. Great collaboration with @elfridedebaere lab and @RAREMED1

[bioRxiv @biorxivpreprint]

Juggling offsets unlocks RNA-seq tools for fast scalable differential usage, aberrant splicing and expression analyses. https://t.co/5pzlmgyRIl #bioRxiv

[VIB Technology Training @VIBTechTraining]

First day of the 4-day BePA Proteomics Summer School @ VIB starting with interesting talks on Proteomics applications and the DOs and DONTs of sample preparation
👉👉 https://t.co/zL3peCo99Z
#proteomics #tech #training #summerschool

[Robbin Bouwmeester @RobbinBouwmees]

DeepLC is out in @naturemethods! Our LC retention time prediction tool for any modification has already shown substantial impact on the analysis of DIA data, proteogenomics, PSM validation, rescoring PSMs... Definitely give it a try for your application! https://t.co/UadyHSbC0e

[Christophe Vanderaa @c_vanderaa]

I'm super proud of my promoter @lgatt0 for winning the BiocAward 2021!! 🥳🏆This is very well deserved !!

[Juan A. Vizcaino @juan_vizcaino]

THANKS to everyone who participated yesterday/today in the @wellcome @emblebi #Proteomics Bioinformatics Course, including the @maxquant team (Christoph, Peli & Jurgen), @lievenClement, @intact team (Birgit & Eliot) & @pride_ebi (@ypriverol,@DeeptiJaiswal, David, Ananth, Shengbo)

[Stephanie Hicks, PhD @stephaniehicks]

Excited to announce that I'm now an Associate Editor for Reproducibility at the Journal of the American Statistical Association 👩‍💻

🔖 https://t.co/s9JoAmP8g2

👀 Want to know more? Check out the JASA Reproducibility Guide: https://t.co/3r7ajr3AM0

[Robbin Bouwmeester @RobbinBouwmees]

Open modification search engine ionbot has the potential to cause a paradigm shift in the proteomics field. Amalgamation of multiple research lines over a decade in the @compomics group that led up to this moment: https://t.co/bi8hp0byeq

[Oliver Stegle @OliverStegle]

Do you like Multi Omics Factor Analysis ? Check out MUON spearheaded by @gtcaa - a software framework that makes multi omics data analysis easy and fun. preprint: https://t.co/WwFUCPLEmJ

Credit to all the methods and software MUON builds on, in particular scanpy!

[lieven clement @lievenClement]

msqrob2 for robust DE analysis of MS-based proteomics is finally available in bioconductor. Thx to all contributors @LudgerGoeminne, Adriaan sticker, @MilanMlft, @lgatt0, & @OllyMCrook https://t.co/vex8sIsrLx

[Jeroen Gilis @GilisJeroen]

*satuRn* is published at @F1000Research! *satuRn* is an R software package for studying differential transcript usage in large (sc-)RNA-seq datasets.

Key features:
- High performance
- Fast
- Accurate FDR control
- Direct transcript-level inference

https://t.co/sdPwzreDPk

[Bioconductor @Bioconductor]

Bioconductor 3.13 is Released!! Thank you to all developers and community members for contributing to the project. See full release announcement: https://t.co/TVyB7z3XRw #rstats @Bioconductor

[Michael Love @mikelove]

{miloR} - Differential neighbourhood abundance testing on a graph

@MDMorgan_cam @emmamarydann

https://t.co/k6Z63j2Wc4

[Federico Marini 🦋@federicomarini.bsky.social @FedeBioinfo]

🥳I'm so excited to say that it is finally time to enjoy a GeneTonic - now in preprint format 🎉🎉🎉
https://t.co/sdW2XZnagh
@AnnekathrinLudt joined the team to deliver a whole set of new features, now it is even easier to combine *all* elements from DE and enrichment 🥃🍹🍸🍺

[Gust Bilcke @Gbilcke]

In our newest paper, we profiled a 48-h diel transcriptome of the benthic diatom Seminavis robusta. Our analysis revealed very high levels of rhythmicity, oscillating lincRNAs, 12-h periodic genes, exciting potential new cell wall genes and much more!

[Rafael Irizarry @rafalab]

Fast and memory-efficient code for performing PCA on Pearson residuals from sparse single cell RNA-Seq data.

1.3 million x 1,000 gene matrix can be done in under 50 seconds on 32GB MacBook.

Starting to add optimized functions for most common tasks here: https://t.co/3PWOyPZhf6

[bioRxiv @biorxivpreprint]

Inverting the model of genomics data sharing with the NHGRI Genomic Data Science Analysis, Visualization, and Informatics Lab-space (AnVIL) https://t.co/8JUSLtQKAs #bioRxiv

[Dylan Rausch @dylanrausch]

Ooh this looks like a way better method of skimming literature than my current method of bookmarking anything interesting on twitter and then never being able to find it again...