goatools
Python library to handle Gene Ontology (GO) terms (by tanghaibao)
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers (by kblin)
| goatools | ncbi-genome-download | |
|---|---|---|
| 2 | 4 | |
| 727 | 891 | |
| - | - | |
| 5.0 | 5.7 | |
| 27 days ago | 10 months ago | |
| Python | Python | |
| BSD 2-clause "Simplified" License | Apache License 2.0 |
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.
goatools
Posts with mentions or reviews of goatools.
We have used some of these posts to build our list of alternatives
and similar projects.
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Confused about gene name/id formats when doing enrichment with goatools
I'm trying to do enrichment analysis with goatools for the first time in my life, and I have no idea what I'm doing. (I'm a computer scientist with practically no bio background).
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Cytoscape & GO
I eventually moved on to use this: https://github.com/tanghaibao/goatools
ncbi-genome-download
Posts with mentions or reviews of ncbi-genome-download.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2022-08-02.
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I have a question about the FTP of annotation files from NCBI's Genbank and RefSeq
If you have the taxonomic IDs of your organisms of interest, there are existing parallelized download tools that are more efficient like https://github.com/kblin/ncbi-genome-download or bit-dl-ncbi-assemblies from https://github.com/AstrobioMike/bit
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Bioinformatics without a lab
Downloading from NCBI can be pretty wonky though, but third parties have made good programs to deal with. As an example - and a personal favorite - you have https://github.com/kblin/ncbi-genome-download which by far is the easiest way to download various assembled genomes.
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Downloading genomes from database via command line FTP
I know you said Ensembl, but if you can live with NCBI, I would suggest https://github.com/kblin/ncbi-genome-download
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Downloading viral genomes programmatically
Useful tool to download from NCBI: ncbi-genome-download
What are some alternatives?
When comparing goatools and ncbi-genome-download you can also consider the following projects:
galaxy - Data intensive science for everyone.
FPL-Defence-Rotations - Best options to rotate defenders in Fantasy Premier League 2023-24
clinker - Gene cluster comparison figure generator