# MicroView
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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](https://microview-bio.readthedocs.io/en/latest/?badge=latest).
## 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):
Raw data
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"description": "# MicroView\n\n<!-- badges: start -->\n\n[](https://github.com/dalmolingroup/microview/blob/master/LICENSE)\n[](https://github.com/dalmolingroup/microview/actions)\n[](https://microview-bio.readthedocs.io/en/latest/?badge=latest)\n\n<!-- badges: end -->\n\nMicroView, a reporting tool for taxonomic classification\n\nMicroView agreggates results from taxonomic classification tools,\nsuch as Kaiju and Kraken, building an interactive HTML report with\ninsightful visualizations.\n\nCheckout the [full documentation](https://microview-bio.readthedocs.io/en/latest/?badge=latest).\n\n## Quickstart\n\nInstall the package:\n\n```sh\npip install microview\n```\n\nAlternatively, you can also install it with Conda:\n\n```sh\nconda install bioconda:microview\n```\n\nGo to your directory containing Kaiju/Kraken-style results and run:\n\n```sh\nmicroview -t .\n```\n\nAlternatively, if you have a CSV table defining result paths and contrasts, like this:\n\n```\nsample,group\nresult_1.tsv,group_one\nresult_2.tsv,group_two\n...etc...\n```\n\nYou can run MicroView like this:\n\n```sh\nmicroview -df contrast_table.csv -o report_with_table.html\n```\n\nThen, an HTML file named `microview_report.html` -\nor the name you defined with the `-o` param -\nshould be available in your working directory,\ntry opening it with your browser!\n\n## Example report\n\nHere's what the beginning of a MicroView report looks like (sensitive information obscured):\n\n\n",
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