Scripts used in Cardiello et al. 2023 Life Science Alliance (https://www.life-science-alliance.org/content/6/8/e202301979) "Evaluation of genetic demultiplexing of single-cell sequencing data from model species"
With 10X Cellranger count and multi generated files, as well as souporcell generated clusters.tsv files, we first read these into R for filtering, correlation analysis and subsequent assignment label renaming, UMAP plotting, and assembling/saving of dataframes for python analysis.
R scripts for this analysis are in this github page and are labelled by figure and species they were used. These R scripts were used to produce the dataframe files needed for python analyses posted below.
Python analysis took place in individual google colab notebooks here:
Zebrafish, axolotl, and green monkey (Figure 1, and Supplemental Figure 1): https://colab.research.google.com/drive/1yXzE3WJ05hEJKdy7owiXOpCjYvUm4DDJ?usp=sharing
Xenopus (Figure 2): https://colab.research.google.com/drive/1lO4ny8Uv9n1lPIbHmZKFPyxWI7gjmZPs?usp=sharing
Pleurodeles (Figure 3): https://colab.research.google.com/drive/1Zbbpi1WwfKGwrrFhuecrHE3lSjP0Pzsz?usp=sharing We have also included the file plasmids.add.to.ref.fa which can be appended to a Pleurodeles reference to map the fluorscent genes for each of the fluorescent Pleurodeles strains.
Pleurodeles and Notophthalmus cellplex (Figure 4): https://colab.research.google.com/drive/12ZNvvfiUt3DL6UpTg8BjQMSd4Y-6yM3u?usp=sharing
Pleurodeles and Notophthalmus barnyard (Supplemental Figure 4): https://colab.research.google.com/drive/1JS8kRUGAioDM2IvYa4oBDzNMKLxBhHV_?usp=sharing