AllenSDK
virnet
AllenSDK | virnet | |
---|---|---|
1 | 1 | |
326 | 29 | |
0.9% | - | |
8.5 | 0.0 | |
4 months ago | over 2 years ago | |
Jupyter Notebook | Jupyter Notebook | |
GNU General Public License v3.0 or later | Apache License 2.0 |
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.
AllenSDK
-
I want to learn how to code over the summer. I am a neuroscience major and I think this skill would make more marketable for labs on campus.
This is a good idea. Neuroscience (at least Systems Neuro) is getting to a point where experiments can generate humongous amounts of data and computational skills are really important for processing it. I would highly recommend Python, although R is great for fitting statistical models and a lot of labs still rely on Matlab. Python is fast becoming the standard though (from what I have seen). The Allen Institute releases tons of data and the AllenSDK for working with it is all in Python. https://github.com/AllenInstitute/AllenSDK
virnet
-
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?
graphein - Protein Graph Library
PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers
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
PPR-Meta - A tool for identifying phages and plasmids from metagenomic fragments using deep learning
MetaRon - Metagenomic opeRon Prediction pipeline. MetaRon presents the first pipeline for the prediction of metagenomic operons without any functional or experimental data.
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
VirusSeeker-Virome - VirusSeeker is a set of fully automated and modular software package designed for mining sequence data to identify sequences of microbial origin.
ViraMiner - CNN based classifier for detecting viral sequences among metagenomic contigs
tolkien-char-prescription-drug - Bilbo, Silenor, Avandaryl, Nardil, Cymbalta. Only one of those is actually a Tolkien character. Could we solve this problem using artificial neural networks?
full_spectrum_bioinformatics - An open-access bioinformatics text