Getting started

To avoid dependency conflicts, we recommend the the use of a dedicated virtual or conda environment. In a terminal run the command:

$ conda create -n ComSeg_env python=3.8
$ conda activate ComSeg_env
$ conda install R=4.3

(Optional) If you want to use a normalization step normalization : then in R do

install.packages("sctransform")
install.packages("feather")
install.packages("arrow")

Alternatively, you can install arrow from conda-forge:

conda install -c conda-forge r-arrow
# or conda install -c conda-forge --strict-channel-priority r-arrow

ComSeg optionally uses sctransform to normalize the expression of “RNA communities”, if you want to use this normalization step, you need to install the R packages. The normalization with sctransform makes the segmentation better.

Download the package from PyPi

Use the package manager pip to install ComSeg. In a terminal run the command:

$ pip install comseg

Clone package from Github

alternatively you can clone the github repository Github repository and install it manually with the following commands:

$ git clone +https://github.com/tdefa/ComSeg_pkg
$ cd ComSeg_pkg
$ pip install -e . -r requirements.txt

for this local install if import comseg as follows:

import src.comseg as comseg

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API reference

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Index

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Support

If you have any question relative to the package, please open an issue on Github.

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