Share this page!

Lior Pachter Profile picture
Twitter logo
Jan 2 • 27 tweets • 8 min read
This flippant comment on #scRNAseq algorithms reflects a common disrespect for computational biologists who are frequently derided for not asking "good biological questions". Moreover, it is peak chutzpah. A short 🧵..
As pointed out by @RArgelaguet, the OP recently coauthored a paper where many #scRNAseq methods, algorithms, and tools were used.. I wonder which of them the OP would have preferred was not developed. @AMartinezArias, please choose from this list:
Bowtie2
nature.com/articles/nmeth…
@anshulkundaje’s genome off-list:
mitra.stanford.edu/kundaje/akunda…
Picard tools
broadinstitute.github.io/picard/
bedtools
academic.oup.com/bioinformatics…
deepTools
academic.oup.com/nar/article/42…
IGV
academic.oup.com/bib/article/14…
kallisto
nature.com/articles/nbt.3…
RNA velocity
nature.com/articles/s4158…
scVelo
nature.com/articles/s4158…
UMAP
nature.com/articles/nbt.4…
scTransform
link.springer.com/article/10.118…
Seurat
satijalab.org/seurat/
Loompy
loompy.org
PCA
tandfonline.com/doi/pdf/10.108…
Wilcoxon test
jstor.org/stable/3001968…
BTW, what was up with thresholding log-fold-change at 0.25? Is that some threshold you made up to get the results you wanted? Speaking of which, why did you choose R instead of Python? Or did you try both?
Seurat “integration”
sciencedirect.com/science/articl…
Cell Ranger v6.0.1
(Unpublished)
Scrublet
sciencedirect.com/science/articl…
Pearson Correlation
(You should probably cite Galton, and also Pearson should be capitalized in your paper)
books.google.is/books?id=JPcRA…
Now @AMartinezArias replied to @RArgelaguet that they did not actually create new algorithms...
But this is false!

"Data analyses of HybISS and subsequent quantification were performed with home-made Python code" 👀
Also what is this? (and BTW it's incompatible with other choices and methods used in the paper).
BTW, the code to generate the analysis in the paper is complex (see all the methods applied in the tweets above!), so I was happy to see it was a posted in a Github repository. Except it’s not there... 👀 github.com/Alev-Lab/axiol…

Please fix ASAP!
h/t @FertigLab who I 100% agree with.

• • •

Missing some Tweet in this thread? You can try to force a refresh
　

Keep Current with Lior Pachter

Lior Pachter Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @lpachter

Lior Pachter Profile picture
Dec 22, 2022
You have to hand it to Lex Fridman. His grift is not an amateur job. Take his Twitter photo. A professor standing in front of a blackboard with some math. Right?
This photo (see RHS of image below) is from what he calls his "MIT course" on Deep Learning for Self-Driving Cars. Sounds like good stuff. CS, math, self driving cars. #broheaven. So what is the problem? He is standing in front of the blackboard.
Well first of all, this was an MIT IAP class. IAP is a short period in January when students get to take fun classes on various topic that can be taught by anyone (many by students). I once sat in on a brain dissection. You can learn how to count cards. web.mit.edu/willma/www/mit…
Read 9 tweets
Lior Pachter Profile picture
Dec 20, 2022
One of the Christmas stories that's almost completely forgotten is that of Bogdanovka. Starting on Dec. 21, 1941, tens of thousands of Jews were murdered in a camp in what is present day Ukraine by Romanian soldiers, ethnic Germans & Ukrainian police. 1/5

timesofisrael.com/romanias-homeg…
Large groups of hundreds of Jews were marched to a ravine in a forest and shot. Those who couldn't manage the march were murdered by the thousands in pigsties in which they were locked that were set on fire. Many others froze to death. degruyter.com/document/doi/1… 2/5
A poignant detail: the murderers took a break to celebrate Christmas, but resumed three days later, having killed ~40,000 people in time for New Years celebrations. 3/5
Read 5 tweets
Lior Pachter Profile picture
Dec 19, 2022
So I got an email from a place called RayTech Group offering me $10,000 per month to write recommendation letters for their students who "need apply universities" with the stipulation that "the content of the recommendation letters can be further discussed" with me.
Their website (raytech.group) says that they achieve "students' comprehensive 'background development'" and "enhance the competitiveness of students at school age. As soon as possible to achieve the Offer from famous universities and enterprises."
This place has a website raytech.group/our.aspx?Class…
with photos of various people affiliated with @Stanford university. E.g. gsb.stanford.edu/faculty-resear…
Read 13 tweets
Lior Pachter Profile picture
Dec 4, 2022
In a new preprint w/@kreldjarn, @DelaneyKSull, @GuillaumOleSan & @pmelsted we address a shortcoming in current approaches to quantifying single-nucleus RNA-seq: biorxiv.org/content/10.110…
tl;dr care has to be taken in quantifying nascent vs. mature transcripts. #snRNAseq #scRNAseq🧵
First, note that single-cell RNA-seq data provides some quantification not only of processed (mature) messenger RNAs, but also of nascent molecules. That observation by @GioeleLaManno, @slinnarsson and colleagues underlies RNA velocity. But what about single-nucleus RNA-seq? 2/
Similarly to #scRNAseq, #snRNAseq data has reads derived from both nascent and mature transcripts. However, perhaps due to intuition that #snRNAseq is all nascent, current approach to quantification yield a single count matrix based on all reads mapping to every gene locus. 3/
Read 16 tweets
Lior Pachter Profile picture
Nov 18, 2022
The "genius" @elonmusk was a year ahead of me @PtaBoysHigh. Every year they gave awards to those "worthy of praise" (digni laude). Perhaps it's not a big surprise that Musk was never deemed "worthy of praise".
Which is fine, of course. Awards like this are rubbish anyway. But friendships aren't, and the people I miss from school, and there are many... are not Musk (in this photo he is front row left).
Nowadays @elonmusk likes to cultivate his genius myth... here his mom gives him an assist. businesstoday.in/latest/trends/…
Read 5 tweets
Lior Pachter Profile picture
Nov 11, 2022
Why are they selling poppies, Mummy?
Selling poppies in town today.
The poppies, child, are flowers of love.
For the men who marched away.
But why have they chosen a poppy, Mummy?
Why not a beautiful rose?
Because my child, men fought and died
In the fields where the poppies grow.
But why are the poppies so red, Mummy?
Why are the poppies so red?
Red is the colour of blood, my child.
The blood that our soldiers shed.
Read 6 tweets

Did Thread Reader help you today?

Support us! We are indie developers!

This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Don't want to be a Premium member but still want to support us?

Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal

Or Donate anonymously using crypto!

Ethereum

0xfe58350B80634f60Fa6Dc149a72b4DFbc17D341E copy

Bitcoin

3ATGMxNzCUFzxpMCHL5sWSt4DVtS8UqXpi copy

Thank you for your support!

Follow Us on Twitter!

Send Email!

:(