|-||2 days ago|
|BSD 3-clause "New" or "Revised" License||GNU General Public License v3.0 or later|
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
We haven't tracked posts mentioning bio-sequence yet.
Tracking mentions began in Dec 2020.
parse a fasta file using regex
2 projects | reddit.com/r/bioinformatics | 28 Sep 2022
Just use Biopython.
Seq: A programming language for high-performance computational genomics
9 projects | news.ycombinator.com | 15 Sep 2021
It might be pretty useful as a teaching tool, but I'm skeptical of its long-term benefit to professionals. I'm not sure the ecosystem of Seq users will be large enough, y'know? Again, it's pretty impressive work, and it's come a long way. I wish the devs all the best. :)
Looking for a tool to convert a whole fasta file with CDS sequences to a fasta file with protein sequences.
3 projects | reddit.com/r/bioinformatics | 8 Aug 2021
Quickly looking over it, that's a bunch of different scripts/functions using https://biopython.org/ to parse FASTA files in different ways. Probably the answer you're looking for is in that txt, or have a look at the Biopython tutorial.
Journey into bioinformatics
2 projects | reddit.com/r/bioinformatics | 28 Apr 2021
For bioinformatics in Python, the BioPython library (https://biopython.org/) is commonly used. An alternative to this package is Biotite (https://www.biotite-python.org/), a package I am maintaining.
Need help with Biopython examples
2 projects | reddit.com/r/bioinformatics | 16 Apr 2021
You can then copy the contents of the file directly ( press Ctrl + A on the webpage, and then Ctrl + C on the text editor you are using ). You can also download the file using a command line tool, such as wget or curl if you are familiar with those. For example, if I wanted to download the ls_orchid.gbk file, I would find the raw version as above and simply open a terminal and type:
What are some alternatives?
RDKit - The official sources for the RDKit library
biotite - A comprehensive library for computational molecular biology
weblogo - WebLogo 3: Sequence Logos redrawn
bioconda-recipes - Conda recipes for the bioconda channel.
Pandas - Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
Numba - NumPy aware dynamic Python compiler using LLVM
PyDy - Multibody dynamics tool kit.
statsmodels - Statsmodels: statistical modeling and econometrics in Python
galaxy - Data intensive science for everyone.
bccb - Incubator for useful bioinformatics code, primarily in Python and R
SciPy - SciPy library main repository
Dask - Parallel computing with task scheduling