Machine Learning framework for prediction of single-cell's chronological age
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GERAS
HumanPancreas
shiny_GERAS_Tf
source
GERAS_Tf_Hs.html
GERAS_Tf_Hs_Final.rds
GERAS_Tf_Zf.html
GERAS_Tf_Zf_Final.rds
README.md
Zf_MultinomialLogisticRegression.R
shiny_GERAS_Tf.R

README.md

GERAS (GEnetic Reference for Age of Single-cell)

Machine Learning Framework for prediction of single-cell's chronological age

The folder contains Rmarkdown reports for generating GERAS for zebrafish beta-cells and human pancreatic cells.

Data for generating and testing the zebrafish model can be found at GEO (GSE109881): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109881

Data for generating and testing the human model can be found in the 'HumanPancreas' folder

Folders contained here are:

source: functions necessary to run GERAS, as well as extract information from developed model.

shiny_GERAS_Tf: files necessary to run the Shiny app. Must be in the same folder as Shiny_GERAS_Tf.R

HumanPancreas: files for training and testing human pancreatic GERAS

Files contained here are:

('Tf' in file names denoted 'Tensorflow', the API used to develop the machine learning framework).

GERAS_Tf_Zf.html: The report from Rmarkdown detailing the steps used for developing zebrafish beta-cell GERAS.

GERAS_Tf_Zf_Final.rds: The GERAS model for zebrafish beta-cells.

GERAS_Tf_Hs.html: The report from Rmarkdown detailing the steps used for developing the human pancreatic GERAS.

GERAS_Tf_Hs_Final.rds: The GERAS model for human pancreatic cells.

shiny_GERAS_Tf.R: R file to run the Shiny app.

Data

Data for generating and testing the zebrafish model can be found at GEO (GSE109881): https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109881

Data for generating and testing the human model can be found in the 'HumanPancreas' folder on Github

The shared data contains:

  1. TrainData: Data for developing GERAS

  2. Zf_GERASStages_Counts.csv: Count values from all stages of zebrafish beta-cells
    Zf_GERASStages_TPM.csv: TPM-normalized values from all stages of zebrafish beta-cells
    Enge_pRPM.csv: RPM-normalized values from human pancreatic cells published in Enge et al., 2017

  3. TestData: Data for testing the GERAS models

  4. Zebrafish Test Data:
    1 mpf beta-cells (new batch)
    13 mpf beta-cells (new batch)
    3 mpf beta-cells sequenced using C1-Chip Fludigm
    4 mpf beta-cells (new batch)
    9 mpf beta-cells
    1.5 mpf beta-cells
    4 mpf beta-cells from animals on intermittent feeding
    4 mpf beta-cells from animals on three-times daily feeding

    Human Pancreatic Test Data:
    Data published in Segerstolpe et al., 2016

Additional Files

Zf_MultinomialLogisticRegression.R: For classification based on a Multinomial Logistic Regression using the nnet package.