bcbio-nextgen
PyDy
bcbio-nextgen | PyDy | |
---|---|---|
2 | 1 | |
973 | 346 | |
0.2% | 0.0% | |
6.2 | 3.9 | |
3 days ago | about 1 year ago | |
Python | Python | |
MIT License | LICENSE.txt |
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.
bcbio-nextgen
-
Deep Sleep May Be the Best Defense Against Alzheimer’s
Re WGS there are a lot of well established tool chains that are FLOSS (eg https://github.com/bcbio/bcbio-nextgen). You could run alignment and variant calling on a beefy workstation. A laptop would potentially work. Easy to test this with publicly available raw data. Another option: The sequencing provider often will run alignment and some default variant calling for you. Annotating and analysing these variants can be done on pretty much any computer, all with open source software. A SNP chip is even easier to deal with as the computational requirements are less.
Interpreting the results is a more manual process. Really depends on what you are interested in.
-
Advices on how to advance in the field to a beginner
There are plenty of workshops and free documentation online, a few from the top of my head : https://hbctraining.github.io/main/, https://software-carpentry.org/lessons/, https://github.com/bcbio/bcbio-nextgen.
PyDy
-
Python for everyone : Mastering Python The Right Way
PyDy (Python Dynamics)
What are some alternatives?
Pandas - Flexible and powerful data analysis / manipulation library for Python, providing labeled data structures similar to R data.frame objects, statistical functions, and much more
SymPy - A computer algebra system written in pure Python
orange - 🍊 :bar_chart: :bulb: Orange: Interactive data analysis
Biopython - Official git repository for Biopython (originally converted from CVS)
Numba - NumPy aware dynamic Python compiler using LLVM
astropy - Astronomy and astrophysics core library
NumPy - The fundamental package for scientific computing with Python.
Dask - Parallel computing with task scheduling
SciPy - SciPy library main repository