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Vivek Rai

Vivek Rai

@raivivek.bsky.social

16 followers 78 following 160 posts

learning biology through code ✨ | migrated from https://x.com/raivivek_

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Vivek Rai @raivivek.bsky.social · Nov 17

years ago, when I was still figuring out my scientific identity as a computational biologist, I stumbled upon Bosco Ho's personal website. it was one of the most beautiful sites I had seen with content that inspired me in many ways. think that's quite fitting for a first post www.boscoh.com #biology

Vivek Rai @raivivek.bsky.social · Mar 11

Hey everyone! I will be migrating from this platform to https://bsky.app/profile/raivivek.bsky.social

Vivek Rai @raivivek.bsky.social · Mar 11

Full text pdf: https://rdcu.be/dsJO7
Explore our data using interactive Shiny dashboard: https://theparkerlab.shinyapps.io/Islet-RNAseq-WGCNA/

#Epigenetics #diabetes #generegulation #bioinformatics

Vivek Rai @raivivek.bsky.social · Mar 11

I wrote a thin wrapper around #Snakemake to help you quickly monitor your Snakemake runs. It simply parses your snakemake logs! Do try - https://github.com/raivivek/snakelog

#bioinformatics #opensource #biology #code #workflows #sequencing #genomics

Vivek Rai @raivivek.bsky.social · Mar 11

#Wikipedia is hosting a "Celebrate Women!" month — help by contributing content, edits, or revisions close to the gender representation gap on Wikipedia. See how you can help: https://meta.wikimedia.org/wiki/Celebrate_Women #WomensMonth

Vivek Rai @raivivek.bsky.social · Mar 11

#TIL (Today I learned) that #Overleaf provides a git interface to your documents! You can compile locally and make changes offline and sync with online version with #git. Honestly, this makes online/offline transition very smooth! #writingtips

Vivek Rai @raivivek.bsky.social · Mar 11

I just donated to @Wikipedia. Support free knowledge! #iloveWikipedia https://donate.wikimedia.org

Vivek Rai @raivivek.bsky.social · Mar 11

Just stumbled upon a website that wouldn't take same first name and last name! Quite ridiculous and reminded me of https://github.com/kdeldycke/awesome-falsehood — a list of #falsehoods #programmers believe in.

Vivek Rai @raivivek.bsky.social · Mar 11

(2 / 2)
1. Visibility is not inclusion
2. There's no such thing as "neutral science"
3. Data-driven approaches are not free of scientific discrimination/racism, and data augmentation is not enough
4. "Neutral decisions" can be neutral to privileged and harmful to non-privileged.

Vivek Rai @raivivek.bsky.social · Mar 11

(1 / 2) Got to learn about important issues on fairness, accountability, and transparency (FAT) in ML (though broadly applicable) from @timnitGebru's excellent talk at @um_midas seminar! Will retweet when recording is available.

My main take away points: (...)

Vivek Rai @raivivek.bsky.social · Mar 11

Feeling excited about my recently acquired Pomodoro timer! #inspired #pomodoro

Vivek Rai @raivivek.bsky.social · Mar 11

> Break the Bubble allows you to find out which books you are statistically unlikely to read. The more narrow your reading tastes are, the more you will be challenged by the results.

https://abooklikefoo.com/escape/

Vivek Rai @raivivek.bsky.social · Mar 11

Thanks @digitalocean! But also thanks to #Bioconda and #conda_forge for accepting my contributions! :D

Vivek Rai @raivivek.bsky.social · Mar 11

I just donated to @Wikipedia. Support free knowledge! #iloveWikipedia https://donate.wikimedia.org/?utm_medium=SocialMedia&utm_campaign=ThankYouPage&utm_source=Twitter&uselang=en

Vivek Rai @raivivek.bsky.social · Mar 11

I was tired of looking up how to convert one bioinformatics format to another, so I created #convert-this-to-that. Work in progress but sneek peek at https://convert.raivivek.in

#bioinformatics #opensource

Vivek Rai @raivivek.bsky.social · Mar 11

I switched from using MS OneNote to simple markdown notes organized in knowledge graphs such as @RoamResearch / @obsdmd a couple of months ago and it has been working out great! Highly recommended as a simple yet powerful #notetaking mechanism. #AcademicChatter #phdchat

Vivek Rai @raivivek.bsky.social · Mar 11

MeetingBar is an excellent free and open-source tool for keeping track of all your virtual meetings! It will sync automatically to your calendar, so no need to manually enter items. #opensource

https://github.com/leits/MeetingBar

Vivek Rai @raivivek.bsky.social · Mar 11

Was browsing GitHub for RStudio themes and stumbled across this repository. Well, thanks for the heads up patrickshox, I won't be using your Mojave Dark theme after all.

https://github.com/patrickshox/Mojave-Dark-RStudio-Theme

Vivek Rai @raivivek.bsky.social · Mar 11

Everyone, please take care of yourself in these extremely difficult and uncertain times.

Vivek Rai @raivivek.bsky.social · Mar 11

#rstats #bioinformatics folks -- what do you prefer for exploratory analysis and quick figures, and why?

Vivek Rai @raivivek.bsky.social · Mar 11

If you enjoy ComplexHeatmap, you might like tidyHeatmap -- a tidy wrapper around ComplexHeatmap. https://github.com/stemangiola/tidyHeatmap #rstats #tidyverse #heatmap #ggplot2

Vivek Rai @raivivek.bsky.social · Mar 11

Please retweet and/or tag people who might have an answer. Thanks!

Vivek Rai @raivivek.bsky.social · Mar 11

Lab that have migrated from hg19 ref to hg38, how did you lead your transition? If not, when you plan to do it? Looking for some #AcademicTwitter #AcademicChatter wisdom! @AcademicChatter

Vivek Rai @raivivek.bsky.social · Mar 11

Install a package for someone, you teach them for a day
Install a package manager, and you teach them for a lifetime.

Vivek Rai @raivivek.bsky.social · Mar 11

My life in 7 pictures. Day 6 of challenge - no words, no people. I was challenged by @theparkerlab :D I challenge everyone to continue focusing on their well being.