full_spectrum_bioinformatics
virnet
| 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 |
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.
full_spectrum_bioinformatics
-
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
-
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.
PhaMers - A bioinformatic tool for identifying bacteriophages using machine learning and k-mers
pydna - Clone with Python! Data structures for double stranded DNA & simulation of homologous recombination, Gibson assembly, cut & paste cloning.
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
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