deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. (by google)
Biopython
Official git repository for Biopython (originally converted from CVS) (by biopython)
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| deepvariant | Biopython | |
|---|---|---|
| 5 | 31 | |
| 3,076 | 4,167 | |
| 1.5% | 2.0% | |
| 9.1 | 9.6 | |
| about 1 month ago | 4 days ago | |
| Python | Python | |
| BSD 3-clause "New" or "Revised" License | GNU General Public License v3.0 or later |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
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.
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.
deepvariant
Posts with mentions or reviews of deepvariant.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-05-06.
- Look over my purchase, is there anything I should return?
- Welche Berufe haben ein riesiges Angebot an Arbeitskräften (zb. Marketing) und welche Berufe haben wirklich echten Fachkräftemangel und brauchen dringend mehr öffentliche Plattform?
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Give me your suggestions for papers with a Convolutional Neural Network in Bioinformatics
See https://www.nature.com/articles/nbt.4235 for the paper and https://github.com/google/deepvariant for the code.
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[D] Is deep learning having an impact in life sciences yet?
Deepvariant is a another example.
Biopython
Posts with mentions or reviews of Biopython.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-05-12.
- Invitación a proyecto - Biopython en Español
- Biopython – Python Tools for Computational Molecular Biology
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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.
- Can you run ScanProsite locally?
- How to iterate over the whole GRCh38 genome with python?
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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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Biology related exercices and "challenges" to train by myself
I think you mind find something of a community around BioPython, which might be helpful. Just looking at the capabilities will probably be instructive as well.
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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.
What are some alternatives?
When comparing deepvariant and Biopython you can also consider the following projects:
galaxy - Data intensive science for everyone.
RDKit - The official sources for the RDKit library
masurca
biotite - A comprehensive library for computational molecular biology
scanpy - Single-cell analysis in Python. Scales to >1M cells.
bioconda-recipes - Conda recipes for the bioconda channel.
transformers - 🤗 Transformers: State-of-the-art Machine Learning for Pytorch, TensorFlow, and JAX.
Numba - NumPy aware dynamic Python compiler using LLVM
af2complex - Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
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
slivar - genetic variant expressions, annotation, and filtering for great good.
PyDy - Multibody dynamics tool kit.