#BioConductor

I thought I was learning how to curate microbiome studies. Turns out, I was also learning how to question research, spot inconsistencies, defend decisions with evidence, and collaborate with people across the world. Three weeks with @Outreachy and @Bioconductor’s BugSigDB 🦠

Beyond the technical work, I experienced the beauty of open source: asking questions, sharing feedback, learning together, and growing as a community. Grateful for the mentors @svetlana_up, @anne_mariesharp, @tohseenn

and fellow contributors who made this journey special. ❤️ Three weeks down, and I’m just getting started! #Outreachy #BugSigDB #Bioconductor #OpenScience

Happy to share an early version of Sig-Bio-Shiny - an application interface for doing Significant Biology on a set of Gene (for 1700+ organisms). Completely made using #R and #Bioconductor. No manual database dump required which make deployment simple. 1/3

The tidyomics ecosystem: enhancing omic data analyses. #OmicsData #Bioconductor #TidyR @TonyPapenfuss @mikelove @steman_research @naturemethods

If you've ever been dazed by design matrices or confused by contrasts when performing gene expression analysis in limma, the new article by Charity Law is for you #bioconductor #rstats (1/2)

📣 We're redesigning the #Bioconductor website and we need YOUR input! Whether you're a wet lab biologist, expert developer or other, your perspectives will shape Bioconductor's future. Takes 5-10 minutes. Closes June 23. ➡️ #Bioinformatics #rstats

Here is a video of yesterday's "Tidy Genomic Analysis Workshop" with @steman_research and myself, highlighting tidy transcriptomics and tidy genomic range manipulation. See video description for workshop materials and links. #rstats #tidy #bioconductor

Finally designed a logo for my #Bioconductor package sSNAPPY( a pathway perturbation testing method! Idea came from a key function that visualises significantly perturbed biological pathways as a network, where node colors reflect directions of change.

#Complexheatmap visualization #rstudio #Bioconductor @iMetaScience @jokergoo_gu @wileymicrobio

Stop using biocLite(). Instead: 1. Install BiocManager from CRAN. 2. Install Bioconductor or CRAN packages with one command: BiocManager::install(c("limma", "knitr")) More info: #Bioconductor #Rstats #bioc2018

Submitted "TREG" my first #Bioconductor package today!!! 🎉 This has been a fun and challenging process. Shout out to @lcolladotor for a ton of guidance 😎 Check out our work finding Total RNA Expression Genes here:

Registration is now open for the 2nd Africa-specific "Introduction to hands-on #Bioconductor" virtual workshop in collaboration with H3Africa, @H3ABioNet , and the Bioconductor Community from 17-19 November. Attendance is free. More information here

It's a small thing, but I have my first package on #Bioconductor (devel) called HPAStainR! It allows individuals to query multiple proteins/genes to see what cell types in the @ProteinAtlas they stain. It is also a Shiny App: #rstats #genomics #shinyapp

#MyYearInReview #2019 👩‍💻 8 invited confs / workshops 📦 6 #Bioconductor #rstats pkg 📖 5 papers accepted / pub 🗣 4 invited dept seminars 💰 4 grants awarded 📊 4 committees 🆕 2 postdocs joined my group 🆕 2 PhD students rotating 🙃 and 1 puppet Stephanie!

I'm thrilled to share our new #Bioconductor package, nipalsMCIA, which performs multi-omic dimensionality reduction using the NIPALS algorithm. It is fast (especially for large datasets), and user friendly. Give it a try! (1/4)

Our new #bioconductor R package 'APL' by @ela_gralinska, @ClemensKohl, and Martin Vingron @VingronLab is out! 'APL' implements the concept of Association Plots for #SingleCell data.

Tooting my own horn time. Here is the class material for my Stats for Neuroscientists course which uses image analysis to talk about experimental design and statistical considerations. It uses the image analysis packages in #Bioconductor and #rstats.

Found this really nice timeline about the history of #rstats. It is very interesting how #bioconductor is created just one year after the stable version of R. And RStudio first release happens only in 2011, 4 years after Hadley's ggplot2! Source:

Orchestrating Single-Cell Analysis with #Bioconductor Preprint: Book: #Rstats

Phew — after two years of development, revisions, and persistence, our paper is finally online! 📄 Publication: [ 📦 Bioconductor package: [ #rhinotypeR #Rpackage #Bioconductor #rhinovirus #publication

Happy to share that #r2u now provides #Ubuntu 24.04, #BioConductor 3.19, and of course #Rstats 4.4.0. 20.7k CRAN packages, and 400+ BioConductor packages as `apt` binaries. #r2u: Fast. Easy. Reliable. Pick All Three.