dash-cytoscape
Biopython
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dash-cytoscape | Biopython | |
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1 | 31 | |
566 | 4,120 | |
1.9% | 4.6% | |
9.3 | 9.6 | |
9 days ago | 1 day ago | |
Python | Python | |
MIT License | GNU General Public License v3.0 or later |
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dash-cytoscape
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Biopython
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comparing the similarity between a set of protein sequences
Usearch will do all-against-all comparisons, cluster sequences, and produce alignments for each cluster. You can set the clustering threshold (proportion of residues identical). The alignments are in fasta format, which is pretty standard. If all you want is basic similarity it might be easiest to just write something that calculates normalized Hamming distances (typically called p-distances in the molecular evolution literature) between pairs of sequences. I suspect the biopython fasta reader (you can install biopython from https://biopython.org/) will be good enough.
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u/Responsible-Gas3852 comments on "Why is Cancer so Hard to Cure?"
Yes, the computing tool for biological computation.
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My boss is considering letting me take a programming course if I have some good reasons why.
Beside that their core lectures to non-computer scientists are public (survey), workshops by software carpentry move around the globe. Maybe your intent to seed hands-on knowledge is in similar tune before heading for biopython, bioperl, bioawk. It doesn't hurt to tap into resources initially written for non-labrats either, e.g. about regular expressions by programming historian.
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Help they’re turning me into a programmer
Well, what language do you want to learn? What is your background so far? Assuming it is more on the side of biology, software carpentry's Python may eventually lead to biopython? Though there equally is a chance for AWK (Hack the planet's text! and bioawk...
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Joining the Open Source Development Course
Python is the main programming language I use nowadays. In particular numpy and pandas are of course extremely useful. I also use biopython package - a collection of software tools for biological computation written in Python by an international group of researchers and developers.
- osdc-2023-assignment1
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parse a fasta file using regex
Just use Biopython.
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Seq: A programming language for high-performance computational genomics
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. :)
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Looking for a tool to convert a whole fasta file with CDS sequences to a fasta file with protein sequences.
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.
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Journey into bioinformatics
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.
What are some alternatives?
RDKit - The official sources for the RDKit library
biotite - A comprehensive library for computational molecular biology
bioconda-recipes - Conda recipes for the bioconda channel.
Numba - NumPy aware dynamic Python compiler using LLVM
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
PyDy - Multibody dynamics tool kit.
weblogo - WebLogo 3: Sequence Logos redrawn
cytoscape.js-dagre - The Dagre layout for DAGs and trees for Cytoscape.js
django-plotly-dash - Expose plotly dash apps as django tags
statsmodels - Statsmodels: statistical modeling and econometrics in Python
bccb - Incubator for useful bioinformatics code, primarily in Python and R
bcbio-nextgen - Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis