Mass spectrometry analysis of cell-type specific brain-derived extracellular vesicle pulldowns

Modules

config.py

• Contains several global variables.

specificity_functions.py

• Calculates various statistical measures of specificity, including tau score, tissue specificity index, gini coefficient, Shannon entropy, specificity measure, and zscore.

Required Packages

• numpy
• pandas
• scipy

brainrnaseq_specificity.py

• Uses data collected and made available by BrainRNA-Seq to determine proteins that are specific to a cell type of interest.

Required Packages

• requests
• numpy
• pandas
• io
• pathlib

Required Documentation

• config
• specificity_functions

gtex_specificity.py

• Uses data made available by GTEx to determine proteins that are specific to the brain.

Required Packages

• pandas

Required Documentation

• specificity_functions
• config

deeptmhmm_localization.py

• Uses the DeepTMHMM deep learning model to identify the most likely subcellular localization of proteins of interest.

Required Packages

• biolib
• gzip
• os
• pathlib
• pandas