All the functions to implement MarkerCount are defined in the python3 script, marker_count.py
, where the two key functions are
MarkerCount()
: marker-based cell-type identifierMarkerCount_Ref()
: reference-based cell-type identifierOne can import the function by adding a line in your script, i.e., from MarkerCount.marker_count import MarkerCount_Ref, MarkerCount
MarkerCount can be installed using pip command. With python3 installed in your system, simply use the follwing command in a terminal.
pip install MarkerCount
Once it is installed using pip, you can import the two functions using the following python command.
from MarkerCount.marker_count import MarkerCount_Ref, MarkerCount
(Installed using pip) You also can import and use MarkerCount in R, for which you need the R package reticulate
.
First, import MarkerCount using the following command
library(reticulate)
mkrcnt <- import("MarkerCount.marker_count")
Then, you can call the MarkerCount functions as follows.
df_res <- mkrcnt$MarkerCount( .. arguments .. )
: marker-based cell-type identifierdf_res <- mkrcnt$MarkerCount_Ref( .. arguments .. )
: reference-based cell-type identifierThe arguments to pass and the return value are the same as those in python.
R example codes is in the Jupyter notebook file cell_id_R_example_v04.ipynb
We provide example usage of MarkerCount in Jupyter notebook file cell_id_example_v03.ipynb
, where you can see how to import and how to run MarkerCount, both in reference-based and marker-based mode. For quick overveiw of the usage of MarkerCount, simply click cell_id_example_v03.ipynb
above in the file list.
To run the example, please download the script, Jupyter notebook file, maker matrix in .csv
file and the two sample single-cell RNA-Seq data with .h5ad
file extension (they are the two data we used in our paper mentioned above) and follow the instruction below.
cell_id_example_v03.ipynb
To run MarkerCount, you need the python packages Numpy
, Pandas
, sklearn
and scipy
.
scanpy
and plotly
are required only to show the results, not for the MarkerCount itself.
All of them can be installed simply using pip
command.
Send email to syoon@dku.edu for any inquiry on the usages.