Ian Dryg's repositories
genelowercase
A script to convert every gene name to capitalized first letter, every other letter lowercase. This is to convert a gene set for GSEA. https://www.gsea-msigdb.org/gsea/index.jsp March 2021 - Ian Dryg
PixelDistance
Using multi-channel microscopy images, calculates the minimum distance between two markers. In this case, it was used to calculate how invasive tumor cells were in lymph nodes by measuring the minimum distance between tumor-positive pixels and pixels positive for a lymphatic vessel marker (LYVE-1).
fgsea_plotupdown
A modified version of plotEnrichment() from FGSEA. This version takes in two pathways instead of one: an UP and a DOWN -regulated pathway. Both are plotted on the same enrichment plot.
good-neighbors
Identify neighborhoods based on local cell populations.
ome_convert_deid
Convert from qptiff (and scn?) to ome tiff and remove some metadata.
VCA
Vertex Component Analysis in Python