pcarbo
Research Assistant Prof, Human Genetics, U. Chicago; previously, Staff Scientist at Ancestry, postdoc & HFSP fellow at U. Chicago, & Ph.D. at UBC
University of ChicagoChicago, IL
Pinned Repositories
bmapathway
MATLAB source code to accompany the PLoS Genetics paper, "Integrated enrichment analysis of variants and pathways in genome-wide association studies indicates central role for IL-2 signaling genes in type 1 diabetes, and cytokine signaling genes in Crohn's disease".
cfw
R code implementing QTL mapping of physiological, behavioral and gene expression phenotypes in Carworth Farms White (CFW) outbred mice.
dotfiles
Files for setting up shell environment on my MacBook and the compute clusters I regularly use.
lbfgsb-matlab
A MATLAB interface for L-BFGS-B
lps
Analysis of LPS (bulk) RNA-seq data from Chevrier lab.
pcarbo
Source code I have shared and analyses I have done.
varbvs
Large-scale Bayesian variable selection for R and MATLAB.
fastTopics
Fast algorithms for fitting topic models and non-negative matrix factorizations to count data.
mixsqp
R package for fast maximum-likelihood estimation of mixture proportions using SQP.
workflowr
Organize your project into a research website
pcarbo's Repositories
pcarbo/varbvs
Large-scale Bayesian variable selection for R and MATLAB.
pcarbo/pcarbo
Source code I have shared and analyses I have done.
pcarbo/lps
Analysis of LPS (bulk) RNA-seq data from Chevrier lab.
pcarbo/cNMF
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
pcarbo/colab
Explorations of the Google Colaboratory.
pcarbo/mr-ash
A simple implementation of the "multiple regression adaptive shrinkage" model, with examples.
pcarbo/mr-mash
A simple implementation of the multivariate multiple regression method with adaptive shrinkage priors ("mr-mash"), with examples.
pcarbo/pcarbo.github.io
Personal website
pcarbo/aRchaic
Exploration, clustering, visualization and classification of DNA damage patterns
pcarbo/binder_test
Specifying a conda environment with `environment.yml`
pcarbo/ctwas
package for the causal TWAS project
pcarbo/dlbayes
Scalable Bayesian variable selection
pcarbo/dogs
Minimal illustration of Binder for sharing a data analysis in R.
pcarbo/ebpmf.alpha
Empirical Bayes Poisson Matrix Factorization
pcarbo/flashier
A faster and angrier package for EBMF. In progress.
pcarbo/gwas-demos
Some R code used to illustrate basic concepts in genome-wide association studies.
pcarbo/iDEA
Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
pcarbo/Infernape
Identify and quantify 3'UTR peaks from scRNA-seq data
pcarbo/MAPITR
R package for 'MArginal ePIstasis Test for Regions' (Crawford & Ramachandran Labs)
pcarbo/methClust
Grade of Membership clustering in methylation data.
pcarbo/myproject
workflowr project from tutorial
pcarbo/myproject2
workflowr project from tutorial
pcarbo/pymir
Disorganized collection of my Python utilities
pcarbo/qBio9_stuff
Materials for qBio9 (September 2023).
pcarbo/rnaseq_tutorial
Materials for RNA-Seq tutorial (Oct, 2023).
pcarbo/topicmodels
Fork of the topicmodels R package.
pcarbo/vgapois
A simple implementation of the variational Gaussian approximation for the Poisson-normal model, with examples.
pcarbo/wflow-dogs
Minimal illustration of Binder for sharing a workflowr data analysis in R.
pcarbo/workflowr-spotify
Project for workflowr tutorial.
pcarbo/workflowr-spotify-2