David R. Hill's repositories
Finkbeiner_StemCellReports2015
Datasets and R scripts related to the manuscript "Transcriptome-wide analysis reveals hallmarks of human intestine development and maturation in vitro and in vivo.""
Munera2017
Analysis methods for the manuscript "Manipulation of a conserved BMP-HOX pathway promotes formation of human large intestinal organoids" by Jorge Munera et al. Cell Stem Cell 2017
astrovirus
Evaluating the transcriptional response of human enteroids to astrovirus infection
Hill_HIO_Colonization_2017
Analysis scripts for the manuscript "Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium"
hilldr.github.io
personal website generated via hugo
HIO_microinjection
This protocol describes the measurement of epithelial barrier permeability in real-time following pharmacologic treatment in human intestinal organoids using fluorescent microscopy and live cell microscopy
HLO_eLife2015
Datasets and R scripts related to the manuscript "In vitro generation of human pluripotent stem cell derived lung organoids "
md5_compare
Generate and check MD5 hashes recursively between two directories
Miller_Lung_Organoids_2017
Data analysis code from the manuscript "In Vitro Induction and In Vivo Engraftment of Lung Bud Tip Progenitor Cells Derived from Human Pluripotent Stem Cells" by AJ Miller et al.
Tsai_LGR5_endoderm_2015
Analysis scripts pertaining to the manuscript "LGR4 and LGR5 function redundantly during human endoderm differentiation" by Yu-Hwai Tsai et. al 2015
org_manuscript_template
Biorxiv latex template for implementation in EMACS Org-Mode
permeability_imaging
convert time-lapse VSI-format microscopy images into a table containing the mean, median, minimum, and maximum intensity
SeqRetriever
This R package formats RNAseq gene expression data for easy to read and convenient visual representation.
STM_dual_rnaseq
Evaluating the differential alignment of host and microbe RNA from STM-injected HIOs