bcbio-nextgen
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis (by bcbio)
RDKit
The official sources for the RDKit library (by rdkit)
bcbio-nextgen | RDKit | |
---|---|---|
2 | 3 | |
973 | 2,427 | |
0.2% | 1.8% | |
6.2 | 9.5 | |
7 days ago | 1 day ago | |
Python | HTML | |
MIT License | BSD 3-clause "New" or "Revised" License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
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.
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
Posts with mentions or reviews of bcbio-nextgen.
We have used some of these posts to build our list of alternatives
and similar projects.
-
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.
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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.
RDKit
Posts with mentions or reviews of RDKit.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-05-20.
- rdkit: RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
- Free Solvent Accessible Surface Area
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What to do about GPU packages on PyPI?
I agree. So many times I have had to reinstall rdkit using homebrew and link it again and again. Although, you can now install rdkit via pip: pip install rdkit-pypi
GitHub Issue: https://github.com/rdkit/rdkit/issues/1812#issuecomment-8088...
What are some alternatives?
When comparing bcbio-nextgen and RDKit you can also consider the following projects:
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
Biopython - Official git repository for Biopython (originally converted from CVS)
orange - 🍊 :bar_chart: :bulb: Orange: Interactive data analysis
NetworkX - Network Analysis in Python
Numba - NumPy aware dynamic Python compiler using LLVM
NumPy - The fundamental package for scientific computing with Python.
Dask - Parallel computing with task scheduling