full_spectrum_bioinformatics
virnet
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| full_spectrum_bioinformatics | virnet | |
|---|---|---|
| 1 | 1 | |
| 67 | 29 | |
| - | - | |
| 6.2 | 0.0 | |
| about 2 months ago | over 2 years ago | |
| Jupyter Notebook | Jupyter Notebook | |
| - | Apache License 2.0 |
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full_spectrum_bioinformatics
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Beginner's bioinformatics books for someone without any knowledge in biology?
A former advisor of mine wrote this up a bit ago and I felt it was solid (also a CS major but did some bio work and his text was written with that in mind). https://github.com/zaneveld/full_spectrum_bioinformatics
virnet
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Bad tools that NEED improvement
VirNet: several issues with their dependencies not being available. For fun, you have to read the issue opened on their "requirments.txt". Pointed out bad dependencies, and mentioned that the file "requirments.txt" was mispelled and so didn't match the README. They updated the README to reflect the mispelling, left the bad file name and bad dependencies, and closed the issue.
What are some alternatives?
poly - A Go package for engineering organisms.
metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
pydna - Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers
ermineR - R wrapper for ermineJ
PPR-Meta - A tool for identifying phages and plasmids from metagenomic fragments using deep learning
amazon-genomics-cli-demos - Demos of what can be done with the Amazon Genomics CLI
MetaRon - Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.
Hail - Cloud-native genomic dataframes and batch computing
Cenote_Unlimited_Breadsticks - DEPRECATED: Discover divergent virus sequences, prune flanking cellular sequences, make basic report
DeePhage - A tool for distinguish temperate phage-derived and virulent phage-derived sequence in metavirome data using deep learning
virMine