ermineR
ncbi-genome-download
ermineR | ncbi-genome-download | |
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1 | 4 | |
6 | 890 | |
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0.0 | 5.7 | |
over 1 year ago | 9 months ago | |
R | Python | |
GNU General Public License v3.0 or later | Apache License 2.0 |
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ermineR
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Gene ontology of differentially expressed genes in R
I would recommend ermineJ as thier statistical approach is better suited to overcome issues with how GO is constructed and the imbalance in the sizes of GO terms (sizes meaning the number of genes assigned). They have a graphical, command line interface and an R package link
ncbi-genome-download
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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?
full_spectrum_bioinformatics - An open-access bioinformatics text
galaxy - Data intensive science for everyone.
rhmmer - Simple R utilities for working with HMMER
clinker - Gene cluster comparison figure generator
Baltica - Baltica: integrated differential junction usage
pyfaidx - Efficient pythonic random access to fasta subsequences
orthologr - Genome wide orthology inference and dNdS estimation
gisaid-uploader - Simplified & efficient GISAID interactions.
OpenWorm - Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
Biopython - Official git repository for Biopython (originally converted from CVS)
UPIMAPI - UniProt Id Mapping through API
eggnog-mapper - Fast genome-wide functional annotation through orthology assignment