shackett
I am the Director of Discovery Data science at @calico where my team turns key outputs of basic research (mechanisms and targets) into data science problems.
Calico: @calicoSouth San Francisco
Pinned Repositories
claman
Calico Lipidomics and Metabolomics (CLaM) Analysis provides a suite of functions which support data manipulation, statistical analysis and visualizations of mzrollDB files created by MAVEN.
impulse
Fit phenomenological sigmoid and impulse curves with priors to improve interpretability
romic
romic represents high-dimensional measurements by persistently tracking features, samples, and measurements as a dataset is modified and reformatted. It provides a suite of functions that build on this framework to support data analysis and visualization. These functions are combined into shiny apps tailored to exploratory data analysis.
GSEAMA
Gene Set Enrichment Analysis Made Awesome
CRISPR-Caller
A method for confirming CRISPR knockouts of genes from sanger sequencing data
fluxr
Streamlining analysis of metabolism
mQTL
Testing how genetic variation in a cross between two parental yeast strains impacts the metabolome
simmer
Systematic Identification of Meaningful Metabolic Enzyme Regulation
yeast_metabolism
Integrating metabolomics, proteomics and flux inference to predict metabolic regulation and control
shackett's Repositories
shackett/simmer
Systematic Identification of Meaningful Metabolic Enzyme Regulation
shackett/CRISPR-Caller
A method for confirming CRISPR knockouts of genes from sanger sequencing data
shackett/yeast_metabolism
Integrating metabolomics, proteomics and flux inference to predict metabolic regulation and control
shackett/fluxr
Streamlining analysis of metabolism
shackett/mQTL
Testing how genetic variation in a cross between two parental yeast strains impacts the metabolome
shackett/Aggregator
Combining peptides to predict the relative abundance of proteins
shackett/CancerIO
Integrative omics using primary tumors
shackett/dplyr
dplyr: A grammar of data manipulation
shackett/Drosophila_metabolism
FBA analysis of drosophila metabolism using Vmax and gas-exchange constraints
shackett/impulse
Fit phenomenological sigmoid and impulse curves with priors to improve interpretability
shackett/IsoPeak
Improved compound identification by simultaneously searching for multiple chemical adducts
shackett/MIDAS
shackett/Pancreatic_tumor_metabolomics
Scripts used to compare metabolite concentrations between paired tumor-benign human pancreatic cancer samples.
shackett/shackett
Smaller projects which are either being turned into blog posts, in early development, or are mothballed
shackett/shackett.github.io
My personal website / blog
shackett/shackettMisc
Assorted functions for plotting (ggplot2 themes) and data manipulation
shackett/simplystats.github.io
Simply Statistics on Github
shackett/Thesis