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auto-qpcr

automatedciliameasurements

Pipeline to measure cilia, nuclei, and centrioles and which cilia are close to which nuclei and centrioles using CellProfiler and Python

brainandorganoids

Manipulating data from uscs cell browser to obtain meaningful information for use at McGill.

celltyper

control-ipsc-characterization

datasharing

The Leek group guide to data sharing

deeplearningcnn_diseasestatusclassifier

A keras model to classify microscopy images of WT and Parkin KO IPSC neurons

health-unhealth-classifier-cnn

hmo_parkin_pink_analysis

Analysis workbooks for single cell RNA sequencing, total RNAseq, flow cytometry, secretomics

if_cytosection_organoid_analysis

ipsc_clustering_and_predictive_models

Work space for input data and anlaysis scripts for data table formating, clustering and predictive models used to anlaysis iPSC differentiating to Cortical neurons

jython-macros

Macros in progress including OrgQ, cellQ, HistQ

mimc_scrnaseqworkshop

An overview of single cell RNA sequencing: from cell ranger to annotation in Seurat

orgm

a jython macro to automate to measure the diameter and area of organoids from brightfield images

parsebio_scrnaseq_analysis

Many data sets workbooks for analysis.

phenix

A framework to identify and explore cellular phenotypes in human organoids using a flow cytometry antibody panel.

phenoid_single_cell_flow_cytometry_analysis

pseudotime101

R scripts or workbooks for running example data using velocity or pseudotime with Monocle R

scrna-seq

Machine Learning and DeepLearning models to classify PD from snRNAseq data

scrnabox-1

A pipeline for scRNA

scrnaseq_workflow_humangenetics

R studio workbook for Human Genetics Workbook 2024: From CellRanger Outputs to Annotation

singlecell_workshop

scRNAseq Workflow step by step workbooks

znz_mcgill_adhd

analysis of single cell sequencing data