Analysis of proteomic data was performed using Python code (version 3.9.12) in the Jupyter Notebook environment (v6.4.8)75 that can be accessed via a GitHub repository (https://github.com/krijgsveld-lab/DIA-ME).
The inhomogeneous refractive indices of biological tissues blur and distort single-molecule emission patterns generating image artifacts and decreasing the achievable resolution of single-molecule localization microscopy (SMLM). Conventional sensorless a
Ouro-Tools can be used in command line, in a Python script, or in an interactive Python interpreter (e.g., Jupyter Notebook).To print the command line usage example of each module from the bash shell, please type the following command....
(alternative) Run cellMarkerPipe as a library in your own python codes or in Jupyternotebook For developers, we also provide you a method to use cellMarkerPipe as a python library. Step 0: Import pipeline and define data_dir and work_dir ...
jupyter notebooks (downloaded athttps://github.com/KULL-Centre/FRETpredict) for our experiments. As the rotamer libraries for our dye pair were not available, we performed ∼ 1.2 µs atomistic MD simulations for each dye in the solution. To correctly reproduce the dynamics of the ...
All scripts, functions, and Jupyter Notebook developed for this study are freely available on GitLab: https://gitlab.com/cvejic-group/integrative-scrna-scatac-human-foetal. The repository also contains the gene expression and fragment matrices. Experimental Model and Subject Details Ethics and Tissue...
We also provide a streamlined workflow as a Jupyter Notebook. Note, we tested our code with the following versions of the Python Packages: numpy (1.17.2), pandas (0.23.0), scipy (1.1.0), matplotlib (2.2.2), pynwb (1.1.0), hdmf (1.2.0), and seaborn (0.9.0). Detailed ...
complementarity across the whole length of the barcode for every read in the FASTQ file. Accuracy was determined by counting the occurrence of errors and dividing this by the number of total bases within the total barcodes. This code is provided as a Jupyter Notebook within the TallyNN GitHub...
Jupyter notebook and ipywidgets were used as a front-end to Python. As a first step, two-color images (\({{\rm{Im}}}_{{\rm{DD}}}\) and \({{\rm{Im}}}_{{\rm{DA}}}\)) were registered and corrected for chromatic aberrations using beads of 200 nm diameter (TetraSpec, ...
So, if you have the papers generated by the previously mentioned Jupyter Notebook in the papers.csv file, you can run it as: python 02-download-pdfs-from-csv.py papers.csv Since it is compressed, the source code needs to be extracted. To help with that, there's dataset-generation/...