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Jim Hester

Jim Hester is a Data Scientist / Bioinformatician / Software Engineer


I write about using Unix, R and Programming for Bioinformatics.

About Me

I am a System Analyst / Programmer on the Bioconductor core team. Previously I have worked as a Data Scientist at Explorys and as a Bioinformatician in David Serre's Lab; part of the Genomic Medicine Institute at the Cleveland Clinic.

I am a proficient R, Perl, C++ and Shell programmer but am also experienced with Python, Java, C and Javascript. I have authored a number of R packages as well as made contributions to popular R packages including ggplot2, dplyr, rmarkdown, plyr, knitr, tidyr, roxygen, httr and ggvis open source projects, among others.


Covr - Test Coverage for R Packages

Track and report code coverage for your package and (optionally) upload the results to a coverage service like Codecov ( or Coveralls ( Code coverage is a measure of the amount of code being exercised by the tests. It is an indirect measure of test quality. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/Fortran code.
CRAN, GitHub

Lintr - Static R Code Analysis

Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with Emacs, Vim and Sublime Text.
CRAN, GitHub

Rex - Friendly Regular Expressions

A friendly interface for the construction of regular expressions. (co-authored with Kevin Ushey)
CRAN, GitHub


A framework to create Bootstrap 3 HTML reports from knitr Rmarkdown.
CRAN, GitHub

Gmailr - Access the Gmail RESTful API

An interface to the Gmail RESTful API. Allows access to your Gmail messages, threads, drafts and labels.
CRAN, GitHub


De Novo Assembly of a Field Isolate Genome Reveals Novel Plasmodium vivax Erythrocyte Invasion Genes Hester J, Chan ER, Menard D, Mercereau-Puijalon O, Barnwell J, Zimmerman PZ and Serre D

Maternal Nutrition Induces Pervasive Gene Expression Changes but No Detectable DNA Methylation Differences in the Liver of Adult Offspring Matthew V. Cannon, David A. Buchner, James Hester, Hadley Miller, Ephraim Sehayek, Joseph H. Nadeau, David Serre

Cathepsin B is a novel gender-dependent determinant of cholesterol absorption from the intestine. Wong WP, Altemus JB, Hester JF, Chan ER, Cote JF, Serre D, Sehayek E. J Lipid Res. 2012 Dec 17.

Whole Genome Sequencing of Field Isolates Provides Robust Characterization of Genetic Diversity in Plasmodium vivax. Chan ER, Menard D, David PH, Ratsimbasoa A, Kim S, Chim P, Do C, Witkowski B, Mercereau-Puijalon O, Zimmerman PA, Serre D. PLoS Negl Trop Dis. 2012 Sep;6(9):e1811. Epub 2012 Sep 6.

A novel method for determining microflora composition using dynamic phylogenetic analysis of 16S ribosomal RNA deep sequencing data. Chan ER, Hester J, Kalady M, Xiao H, Li X, Serre D. Genomics. 2011 Oct;98(4):253-9. Epub 2011 Apr 15.

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Serre D, Lee BH, Ting AH. Nucleic Acids Res. 2010 Jan;38(2):391-9. Epub 2009 Nov 11.