11–18 of 18 posts
I feel like this might not be sophisticated enough for bioinformaticians, but too complex for the casual user or clinician. Unfortunately, proper bioinformatics requires a heafty dose of background knowledge. If you don't understand what you are aligning and filtering, and why, then the results will always just be a shot in the dark.
It's times like these that I wish I had a better understanding of biology/chemistry/genetics. I fancy myself a Python/data person, does anyone have any advice on what to read to begin understanding how to utilize a package like this?
[1] https://liorpachter.wordpress.com/2015/11/01/what-is-a-read-...
Apologies for a trivial objection: but the serpentine icon associated with this, likely otherwise fine, package embodies an odd little annoyance to all us structural biochemists: It depicts the DNA helix as left-handed. This is a rare form of DNA at best, most likely an unlucky graphical choice, and causes many nerdy folk to suspect that you don't know what you're doing. If you think i'm nuts (and hey maybe...) there…
Just FYI, I found multiple spelling errors in the documentation and readme. specically -> specifically Therefor -> therefore Instanciating -> Instantiating aned -> and Also the first sentence in the readme isn't grammatically correct. This is a cool library, but I think it's important to have these sorts of things cleaned up :)
Apologies for a trivial objection: but the serpentine icon associated with this, likely otherwise fine, package embodies an odd little annoyance to all us structural biochemists: It depicts the DNA helix as left-handed. This is a rare form of DNA at best, most likely an unlucky graphical choice, and causes many nerdy folk to suspect that you don't know what you're doing. If you think i'm nuts (and hey maybe...) there…
Other nerdy folks will be happy to grant that an icon is merely that and not intended to be a perfect embodiment of a molecule.
As far as I can tell, this is just a python wrapper for common bioinformatics tools? I feel like this might not be sophisticated enough for bioinformaticians, but too complex for the casual user or clinician. Unfortunately, proper bioinformatics requires a heafty dose of background knowledge. If you don't understand what you are aligning and filtering, and why, then the results will always just be a shot in the dark.
PyGeno was already used for two peer reviewed articles:
-Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides. Granados, Sriranganadane, Daouda et al. 2014, Nat. Comm
-MHC I-associated peptides preferentially derive from transcripts bearing miRNA response elements. Granados et al. 2012, Blood
And four others are on the way.
Just FYI, I found multiple spelling errors in the documentation and readme. specically -> specifically Therefor -> therefore Instanciating -> Instantiating aned -> and Also the first sentence in the readme isn't grammatically correct. This is a cool library, but I think it's important to have these sorts of things cleaned up :)
contribute a pull request?
Damn, that's a really cool logo they came up with. Looks to me like combining the snake from the Rod of Asclepius, plus Python, plus the DNA double helix and the mouse snake head (which I'm guessing is supposed to stand represent using computers for medicine). Whoever made it, that's pretty awesome. Oh yeah, the actual package is pretty cool too ;)
That logo is awesome. :)