COVID-19 tracking

by Anthony Greenberg, posted on Apr 6, 2023

I tracked local infection rate data during the COVID pandemic (between 2020 and 2022). I am saving the resulting page here as a historical record. I stopped updating this page on December 20, 2022 after Tompkins County stopped publishing daily data tables.

This page displays plots tracking COVID-19 …

Power and limitations of genetics as a tool to study racial differences

by Anthony Greenberg, posted on Apr 6, 2018

The recent New York Times opinion piece by the geneticist David Reich on genetics of differences between human races has generated much discussion among my scientist friends. It was followed by a rebuttal from 67 scholars of diverse backgrounds, and a sympathetic article by the blogger and essayist …

Fast ordered sampling of SNPs from large files

by Anthony Greenberg, posted on Nov 6, 2017

Ever since I left my academic position and became independent, I have been interested in the idea of using minimal computer resources to perform big-data statistical analyses. I do not have a permanent office, so the only computer I own is a laptop, although it is a close to maximal-spec 15-inch …

Accidental benchmarking of Apple's new file system, APFS

by Anthony Greenberg, posted on Oct 6, 2017

Apple recently released High Sierra, the new version of Mac OS. While it is billed as one of those “stability releases” with few user-facing changes, it introduces a new file system, APFS. This system has already been rolled out for iOS devices. This is not something users interact with …

The Google diversity memo makes an important mistake

by Anthony Greenberg, posted on Aug 6, 2017

The recently-published memo (full text can be found at the end of this article) from a Google employee about the causes of gender disparity in the number of people working at the company generated a lively discussion. The arguments are as wide-ranging as the original post and involve many important …

Quickly extracting SNPs from alignments

by Anthony Greenberg, posted on May 6, 2017

Working on a Drosophila population genetics project, I needed to extract SNPs from a large-ish data set of sequence alignments from the Drosophila Genome Nexus. The alignments are in a slightly strange but handy format: each line and chromosome arm is in a separate file. The sequences are all on one …

Democratic turn-out in the 2016 election

by Anthony Greenberg, posted on Nov 6, 2016

The unexpected election of Donald Trump as the next President of the United States has generated an avalanche of articles and social media posts attempting to explain what went wrong and why the pre-election predictions were so off. This event seems of a piece with the earlier similarly unexpected …