Installation Guide
You can easily install PyCytoDR
from either conda
or PyPI
. We recommend
conda
for its easy environment management, but you can of course use PyPI
if you prefer. Just follow the instructions below and you are good to go!
Conda
You can install our package on conda
:
conda install pycytodata -c kevin931 -c bioconda
Our conda
package is published here.
PyPI
You can also install our package on from PyPI
:
pip install PyCytoData
Our PyPI
package is published on this page.
Dependencies
We try to make this package as lightweight as possible. Thus, as of now, we only depend on three packages:
fcsparser
pandas
numpy
fcsparser
and pandas
are used for handling benchmark datasets and their associated fcs
files.
We use numpy
for all computations and preprocessing.
Optional Dependency
If you wish to perform dimension reduction (DR), you can install CytofDR
and have it integrated into
this package. We know that DR is a pretty common workflow, but we didn’t make it mandatory because
CytofDR
depends on a large number of DR packages, which makes the dependency unnecessarily complex
if one does not wish to perform DR. To install CytofDR
, you can run the following:
pip install CytofDR
Or, with conda
:
conda install -c kevin931 cytofdr -c conda-forge -c bioconda
For detailed documentation on CytofDR
installation, which can get quite tricky if you want to use
its own optional dependencies such as SAUCIE
and GrandPrix
, you can visit its
Installation Guide.