NanoSim
deepvariant
Our great sponsors
| NanoSim | deepvariant | |
|---|---|---|
| 1 | 5 | |
| 213 | 3,078 | |
| 3.3% | 1.5% | |
| 5.6 | 9.1 | |
| about 2 months ago | about 1 month ago | |
| Python | Python | |
| GNU General Public License v3.0 or later | BSD 3-clause "New" or "Revised" License |
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.
NanoSim
-
Raw nanowire sequencer data
Alternatively, you can make your own data using NanoSim. I haven't used it myself yet but it generates signal level files with similar error profiles to the real thing. https://github.com/bcgsc/NanoSim
deepvariant
- 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?
-
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.
-
[D] Is deep learning having an impact in life sciences yet?
Deepvariant is a another example.
What are some alternatives?
bonito - A PyTorch Basecaller for Oxford Nanopore Reads
galaxy - Data intensive science for everyone.
bioinformatics - Bioinformatic algorithms for the UCLA Bioinformatics Specialization
masurca
scanpy - Single-cell analysis in Python. Scales to >1M cells.
transformers - 🤗 Transformers: State-of-the-art Machine Learning for Pytorch, TensorFlow, and JAX.
Biopython - Official git repository for Biopython (originally converted from CVS)
af2complex - Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
slivar - genetic variant expressions, annotation, and filtering for great good.
nni - An open source AutoML toolkit for automate machine learning lifecycle, including feature engineering, neural architecture search, model compression and hyper-parameter tuning.
DnaChisel - :pencil2: A versatile DNA sequence optimizer