UPIMAPI
deepvariant
UPIMAPI | deepvariant | |
---|---|---|
3 | 5 | |
26 | 3,094 | |
- | 1.2% | |
7.5 | 9.1 | |
5 months ago | 2 months ago | |
Python | Python | |
BSD 3-clause "New" or "Revised" License | 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.
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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.
UPIMAPI
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Any programs/packages that will allow me to compare cluster annotations obtained from metagenomic data?
You may run MOSCA (https://github.com/iquasere/MOSCA), it performs all major steps of metagenomics analysis. It includes that functional classification you are looking for, since with UPIMAPI (https://github.com/iquasere/UPIMAPI) it annotates with UniProt DB as reference, and obtains information including taxonomy, EC numbers, and even those GOs, and reCOGnizer (https://github.com/iquasere/reCOGnizer), which annotates with CDD DB as reference, and obtains orthologous groups information (COG, Pfam, etc).
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Metatranscriptomics Workflow Questions?
Prediction of coding sequences takes as input the contigs you obtained, and gives you the translated genes. Besides annotating with the KEGG database, you may also want to annotate with more general purpose databases (e.g. UniProt), as these provide more taxonomies and functional information. MOSCA includes UPIMAPI (https://github.com/iquasere/UPIMAPI) and reCOGnizer (https://github.com/iquasere/reCOGnizer), which annotate genes with reference to UniProt and CDD databases using two different methods, providing complementary information. This is the same methodology used by widely popular tools such as eggNOG-mapper and Prokka, but these use other databases.
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Problems using Prokka
Install with mamba instead of conda, no more problems. Or use UPIMAPI (https://github.com/iquasere/UPIMAPI) together with reCOGnizer (https://github.com/iquasere/reCOGnizer), since these tools obtain better results when annotating proteins
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?
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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.
What are some alternatives?
ncbi-genome-download - Scripts to download genomes from the NCBI FTP servers
galaxy - Data intensive science for everyone.
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
bioinformatics - Bioinformatic algorithms for the UCLA Bioinformatics Specialization
ariba - Antimicrobial Resistance Identification By Assembly