microview
A reporting tool for aggregating results from taxonomic classification analyses
Science Score: 44.0%
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✓CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
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○DOI references
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (10.1%) to scientific vocabulary
Keywords
Repository
A reporting tool for aggregating results from taxonomic classification analyses
Basic Info
- Host: GitHub
- Owner: dalmolingroup
- License: bsd-3-clause
- Language: Python
- Default Branch: main
- Homepage: https://microview-bio.readthedocs.io/en/latest/
- Size: 1.15 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
MicroView
MicroView, a reporting tool for taxonomic classification
MicroView agreggates results from taxonomic classification tools, such as Kaiju and Kraken, building an interactive HTML report with insightful visualizations.
Checkout the full documentation.
Quickstart
Install the package:
sh
pip install microview
Alternatively, you can also install it with Conda:
sh
conda install bioconda:microview
Go to your directory containing Kaiju/Kraken-style results and run:
sh
microview -t .
Alternatively, if you have a CSV table defining result paths and contrasts, like this:
sample,group
result_1.tsv,group_one
result_2.tsv,group_two
...etc...
You can run MicroView like this:
sh
microview -df contrast_table.csv -o report_with_table.html
Then, an HTML file named microview_report.html -
or the name you defined with the -o param -
should be available in your working directory,
try opening it with your browser!
Example report
Here's what the beginning of a MicroView report looks like (sensitive information obscured):
Owner
- Name: Dalmolin Systems Biology Group
- Login: dalmolingroup
- Kind: organization
- Location: Natal, RN - Brazil
- Website: dalmolingroup.imd.ufrn.br
- Repositories: 5
- Profile: https://github.com/dalmolingroup
Research group in Systems Biology at UFRN
Citation (CITATION.cff)
cff-version: 1.0.0
message: "If you use this software, please cite it as below."
authors:
- family-names: Cavalcante
given-names: "João Vitor"
orcid: https://orcid.org/0000-0001-7513-7376
- family-names: "Siqueira Dalmolin"
given-names: "Rodrigo Juliani"
orcid: https://orcid.org/0000-0002-1688-6155
title: "MicroView"
version: 0.11.0
url: "https://github.com/jvfe/microview"
GitHub Events
Total
Last Year
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 1
- Total pull requests: 4
- Average time to close issues: 1 day
- Average time to close pull requests: 11 minutes
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 4
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 1
- Average time to close issues: 1 day
- Average time to close pull requests: 12 minutes
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jvfe (1)
Pull Request Authors
- jvfe (6)
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Dependencies
- actions/checkout v2 composite
- actions/setup-python v2 composite
- psf/black stable composite
- python 3.9.16-slim-buster build