semvec/pypi-packages huggingface dataset:
MicroView 0.11.0
Generate reports from metagenomics data
License: BSD license
Requires Python: >=3.8
Keywords: metagenomics workflow visualization report

# 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):

![MicroView header](https://i.imgur.com/YNRH9yK.png)