Name: calour
Owner: biocore
Description: exploratory and interactive microbiome analyses based on heatmaps
Created: 2016-01-26 19:22:48.0
Updated: 2017-11-28 23:39:23.0
Pushed: 2017-11-21 07:20:12.0
Homepage: null
Size: 22798
Language: Jupyter Notebook
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exploratory and interactive microbiome analysis based on heatmaps
Note: these installation instructions are for Mac/Unix. For Windows installation instructions click here
Create a conda environment for calour:
a create -n calour python=3.5 matplotlib numpy scipy pandas qt jupyter scikit-learn statsmodels
and activate it using:
ce activate calour
Install dependecies of biom-format and scikit-bio:
a install -c biocore biom-format scikit-bio
Install calour:
install git+git://github.com/biocore/calour.git
Install the dbBact calour interface:
install git+git://github.com/amnona/dbbact-calour
Install the phenotype-database calour interface:
(based on : Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information - Barberán et al. 2017)
install git+git://github.com/amnona/pheno-calour
install git+git://github.com/amnona/gnps-calour
If you use calour in Jupyter Notebook, it is highly recommended to install ipywidgets:
a install -c conda-forge ipywidgets
or
install ipywidgets
If you would like to use the graphical user interface, you will need to install the GUI interface EZCalour:
install git+git://github.com/amnona/EZCalour
Full documentation is located here. One strength of Calour is that users can interactivelly explore the data patterns on the heatmap. The key and mouse instructions to explore and manuvor the heatmap is explained here
You can also check out a very simple demo of Calour usage in this Jupyter Notebook. A real use case of Calour on a real microbiome data set is also shown in this Jupyter Notebook.