jonathan dreyfuss's repositories
zero2bioinfo
Tutorial to teach beginners with no programming experience the basics of R and common bioinformatics workflows
ezlimmaplot
R package for plotting bioinformatics results, especially those from the ezlimma package
jdcbioinfo
Miscellaneous R functions helpful for analysis. Not built for public consumption.
viral-insulin-peptides
Supplementary code + data for Altindis et al., Viral insulin-like peptides activate human insulin and IGF-1 receptor signaling: A paradigm for host–microbe interactions, PNAS, 2018.
bioinformd
Generate RMD files for bioinformatic workflow
fat-exosome-microrna
Data/code/output for "Adipose-derived circulating miRNAs regulate gene expression in other tissues" by Thomou, Mori, Dreyfuss, et al. (2017)
pread-brown-white
Code/output from paired analysis of brown vs. white human preadipocytes from Ramirez et al.
DirectionalMaxPTest
Directional MaxP test for replication, mediation, and qualitative interactions
max-accuracy-genetic-pred
Code to accompany the paper "How accurate can genetic predictions be?" by Dreyfuss, Levner, et al.
slimm-t2d-omics
Analyses & data for SLIMM-T2D trial omics
antibiotic-stool-proteomics
Proteomics from stool of mice, some of whom received antibiotics
bioage
Calculates biological ages using a standard algorithm.
celiac-gut-microbiome
Data and analysis of gut microbiome in celiac disease
CIT
Causal Inference Test
fast-automated-recon-metabolism
Matlab code and data to reproduce results from "Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM" by Dreyfuss, Zucker, et al.
Foxk12-insulin
Data for "FoxK1 and FoxK2 in Insulin Regulation of Cellular and Mitochondrial Metabolism" (Nature Communications, 2019)
hitman-supp
Supplementary note describing the Hitman algorithm and its validation
iglu
R package for Interpreting GLUcose data from CGMs (Continuous Glucose Monitors)