SigProfilerExtractor
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting. (by AlexandrovLab)
Biopython
Official git repository for Biopython (originally converted from CVS) (by biopython)
| SigProfilerExtractor | Biopython | |
|---|---|---|
| 1 | 31 | |
| 146 | 4,185 | |
| 2.7% | 1.6% | |
| 3.5 | 9.6 | |
| 17 days ago | 5 days ago | |
| Python | Python | |
| BSD 2-clause "Simplified" 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.
SigProfilerExtractor
Posts with mentions or reviews of SigProfilerExtractor.
We have used some of these posts to build our list of alternatives
and similar projects.
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Any good tutorials/guides for cancer mutation analysis?
Ludmil Alexandrov's tools may be a better modern choice for real data though: https://github.com/AlexandrovLab/SigProfilerExtractor
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 SigProfilerExtractor and Biopython you can also consider the following projects:
sv-callers - Snakemake-based workflow for detecting structural variants in genomic data
RDKit - The official sources for the RDKit library
deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
biotite - A comprehensive library for computational molecular biology
scispacy - A full spaCy pipeline and models for scientific/biomedical documents.
bioconda-recipes - Conda recipes for the bioconda channel.
scanpy - Single-cell analysis in Python. Scales to >1M cells.
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
statsmodels - Statsmodels: statistical modeling and econometrics in Python
SigProfilerExtractor vs sv-callers
Biopython vs RDKit
SigProfilerExtractor vs deepvariant
Biopython vs biotite
SigProfilerExtractor vs scispacy
Biopython vs bioconda-recipes
SigProfilerExtractor vs scanpy
Biopython vs Numba
Biopython vs Pandas
Biopython vs PyDy
Biopython vs weblogo
Biopython vs statsmodels