Pierre Marijon
@pierre-marijon.bsky.social
Research engineer, #bioinformatics, #genomic, #assembly, #variantcalling he|him #BiInSci #dyslexic #disabled
https://pierre.marijon.fr/link.html
https://pierre.marijon.fr/link.html
Reposted by Pierre Marijon
#rustbio 3.0 is released, providing BEDPE support and an improved API for Myers bitparallel pattern matching. github.com/rust-bio/rus...
GitHub - rust-bio/rust-bio: This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via cont...
This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration. - rus...
github.com
September 19, 2025 at 1:01 PM
#rustbio 3.0 is released, providing BEDPE support and an improved API for Myers bitparallel pattern matching. github.com/rust-bio/rus...
I have the impression that I'm the only one who wanted to load multiple data tracks in igv with one bedgraph.
I discovered it wasn't possible.
It seems easy to me to use each column of the bedgraph to make an igv track but as usual in this kind of case I must miss something.
#bioinformatics
I discovered it wasn't possible.
It seems easy to me to use each column of the bedgraph to make an igv track but as usual in this kind of case I must miss something.
#bioinformatics
July 17, 2025 at 2:45 PM
I have the impression that I'm the only one who wanted to load multiple data tracks in igv with one bedgraph.
I discovered it wasn't possible.
It seems easy to me to use each column of the bedgraph to make an igv track but as usual in this kind of case I must miss something.
#bioinformatics
I discovered it wasn't possible.
It seems easy to me to use each column of the bedgraph to make an igv track but as usual in this kind of case I must miss something.
#bioinformatics
Reposted by Pierre Marijon
I used to be a proto-mover.
Then, I read and wrote text files.
Wondering what's next.
www.reddit.com/r/bioinforma...
Then, I read and wrote text files.
Wondering what's next.
www.reddit.com/r/bioinforma...
May 15, 2025 at 2:03 PM
I used to be a proto-mover.
Then, I read and wrote text files.
Wondering what's next.
www.reddit.com/r/bioinforma...
Then, I read and wrote text files.
Wondering what's next.
www.reddit.com/r/bioinforma...
Variant normalisation are left align, HGVS Nomenclature are 3' align.
CRY IN BIOINFORMATICS !
CRY IN BIOINFORMATICS !
April 18, 2025 at 9:04 AM
Variant normalisation are left align, HGVS Nomenclature are 3' align.
CRY IN BIOINFORMATICS !
CRY IN BIOINFORMATICS !
Reposted by Pierre Marijon
Playing with #vizitig again to prepare for the 1.0 release. This is the SNAP25 human gene expressed in 3 SRA datasets linked to cancers.
Exons have one color each, and exon junctions are in yellow.
The rest is new/noise.
Exons have one color each, and exon junctions are in yellow.
The rest is new/noise.
March 26, 2025 at 8:33 PM
Playing with #vizitig again to prepare for the 1.0 release. This is the SNAP25 human gene expressed in 3 SRA datasets linked to cancers.
Exons have one color each, and exon junctions are in yellow.
The rest is new/noise.
Exons have one color each, and exon junctions are in yellow.
The rest is new/noise.
A new release of niffler thank to
@luizirber.bsky.social
to say we must create a crate from my piece of code 6 year ago !
#rustlang
@luizirber.bsky.social
to say we must create a crate from my piece of code 6 year ago !
#rustlang
New release! niffler 3.0.0 is out!
crates.io/crates/niffl...
niffler is an utility crate to make it easy to work with compressed data.
For this release we worked on simplifying how features are activated for specific formats, giving more control to users (and less maintenance burden for us =])
🧵
crates.io/crates/niffl...
niffler is an utility crate to make it easy to work with compressed data.
For this release we worked on simplifying how features are activated for specific formats, giving more control to users (and less maintenance burden for us =])
🧵
crates.io: Rust Package Registry
crates.io
February 12, 2025 at 5:44 PM
A new release of niffler thank to
@luizirber.bsky.social
to say we must create a crate from my piece of code 6 year ago !
#rustlang
@luizirber.bsky.social
to say we must create a crate from my piece of code 6 year ago !
#rustlang
Reposted by Pierre Marijon
Sometimes I spent 1 hour on my sunday evening to made clever change (const generic rust magic) and when I proof read my own PR, my reaction is:
It's clever, it's pretty, but it doesn't improve perf and it can create many problems. In fact, if I reviewed this PR, I'd probably reject it..
It's clever, it's pretty, but it doesn't improve perf and it can create many problems. In fact, if I reviewed this PR, I'd probably reject it..
February 9, 2025 at 9:55 PM
Sometimes I spent 1 hour on my sunday evening to made clever change (const generic rust magic) and when I proof read my own PR, my reaction is:
It's clever, it's pretty, but it doesn't improve perf and it can create many problems. In fact, if I reviewed this PR, I'd probably reject it..
It's clever, it's pretty, but it doesn't improve perf and it can create many problems. In fact, if I reviewed this PR, I'd probably reject it..
I think I can say if you want identify which genomic annotation overlap a variant superinterval are fast I didn't realy understand how but it's fast #rustlang #bioinformatics
(source code of benchmark: github.com/natir/clairi...)
(source code of benchmark: github.com/natir/clairi...)
January 23, 2025 at 2:22 PM
I think I can say if you want identify which genomic annotation overlap a variant superinterval are fast I didn't realy understand how but it's fast #rustlang #bioinformatics
(source code of benchmark: github.com/natir/clairi...)
(source code of benchmark: github.com/natir/clairi...)
It seems that one of my colleague's excel is still having a problem with the dates. This is the first time I've seen a genotype to date conversion.
January 3, 2025 at 9:26 AM
It seems that one of my colleague's excel is still having a problem with the dates. This is the first time I've seen a genotype to date conversion.