jdreyf Goto Github PK

antibiotic-stool-proteomics

Proteomics from stool of mice, some of whom received antibiotics

bioage

Calculates biological ages using a standard algorithm.

bioinformd

Generate RMD files for bioinformatic workflow

celiac-gut-microbiome

Data and analysis of gut microbiome in celiac disease

cit

Causal Inference Test

directionalmaxptest

Directional MaxP test for replication, mediation, and qualitative interactions

ezlimma

R package that streamlines & extends limma for linear modeling of omics data

ezlimmaplot

R package for plotting bioinformatics results, especially those from the ezlimma package

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.

fat-exosome-microrna

Data/code/output for "Adipose-derived circulating miRNAs regulate gene expression in other tissues" by Thomou, Mori, Dreyfuss, et al. (2017)

foxk12-insulin

Data for "FoxK1 and FoxK2 in Insulin Regulation of Cellular and Mitochondrial Metabolism" (Nature Communications, 2019)

hitman

High-throughput mediation analysis (Hitman)

hitman-supp

Supplementary note describing the Hitman algorithm and its validation

iglu

R package for Interpreting GLUcose data from CGMs (Continuous Glucose Monitors)

jdcbioinfo

Miscellaneous R functions helpful for analysis. Not built for public consumption.

max-accuracy-genetic-pred

Code to accompany the paper "How accurate can genetic predictions be?" by Dreyfuss, Levner, et al.

pread-brown-white

Code/output from paired analysis of brown vs. white human preadipocytes from Ramirez et al.

screendmt-dihome-replication

Data analysis to reproduce results from biorxiv paper

slimm-t2d-omics

Analyses & data for SLIMM-T2D trial omics

stat

sybilxf

R package for integration of Seahorse extracellular flux (XF) data with metabolic modeling utilizing the R modeling package sybil.

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.

zero2bioinfo

Tutorial to teach beginners with no programming experience the basics of R and common bioinformatics workflows

zero2bioinfo-interactively