caseywdunn

Using samtools

This is my own exploration of samtools behavior and snippets of code I use in my own analyses.

The data

I am using the GRCh38 human reference from December, 2013.

There are two focal datasets of reads:

• Nanomia, NA19 V3698-D2. SRR23143273

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Some links...

Phylogenetic Biology, a book

Statistical Modeling: The Two Cultures

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Rust cheatsheet

Some notes as I learn Rust.

Learning the Rust language

• The Rust Programming Language

• The Rust Performance Book

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# The catalytic converter theft chain

Just had the second attempted theft of our catalytic converter. Here is a bit about context.

## Theft and fencing

https://youtu.be/ZGLrRj7AJsc?t=172

I am not sure at what point the contraband enters the legitimate supply chain.

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Data Visualization

Some basic notes for a couple hour discussion about data visualization.

Build on a few points from my previous course.

To read in advance of the class: https://r4ds.had.co.nz/data-visualisation.html .

Agenda

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Harvard Systems Biology Theory Lunch

Short url: https://git.io/fjchB

10 May 2019

Casey Dunn

Animal diversity and the Hubble deep field

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Postdoc position: HIV phylogenetics at Yale University

Please share this link to the ad: https://git.io/yale_postdoc_2018

Advisor: Casey Dunn

Location: Department of Ecology and Evolutionary Biology, Yale University, in New Haven, Connecticut, USA

Application due date: June 1, 2018 (or until filled)

caseywdunn

Working with Conda

First, some nomenclature (see https://conda.io/docs/glossary.html for more):

• A recipe is a flat directory that has the information needed to build a package
• A package is a "compressed file that contains everything that a software program needs in order to be installed and run... You manage conda packages with conda."
• An environment is a "directory that contains a specific collection of conda packages and their dependencies, so they can be maintained and run separately without interference from each other."

A typical workflow:

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These examples of regular expressions are taken largely from our book Practical computing for Biologists. More information is available at http://practicalcomputing.org.

This document can be accessed via the delightful github url shortener at https://git.io/dine

Given the following names:

Agalma elegans

Frillagalma vitiazi

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Evolution 2017

June 25, 2017 (and updated since then)

Casey Dunn, http://dunnlab.org , @caseywdunn

These are some notes and annotated references relevant to my talk with Stacey Smith in the symposium "SSB Symposium Phylogenetic approaches to connecting genotypes to phenotypes" at Evolution 2017.

If you are interested in any of this work let me know. I am moving to Yale and looking for people to join the new research group.