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followers: 25.0 following: 7.0 repos: 34.0 gists: 0.0

Name: Bradley Martin

Type: User

Bio: I am a population geneticist and bioinformatician with experience in Python, R, and Linux BASH shell.

Twitter: turtlePowerYo

Location: Arkansas

Hi there!
I'm Bradley T. Martin, PhD
Bioinformatician, Data Scientist,
Evolutionary Biologist, and Population Geneticist

Follow me on Twitter!

✉️ [email protected]

I earned my Ph.D. in Biological Sciences, focusing on evolutionary biology and population genomics. While pursuing my doctorate, I developed a love for programming. Currently, I work as a bioinformatician and data scientist, specializing in developing machine learning software to process and analyze short-read and long-read genomic data.

I enjoy learning and new challenges and greatly enjoy my work. For personal projects, I am currently developing several new software to implement machine learning into population genomic analyses, which shows promise for resolving long-standing issues involving introgression, species delimitation, and phylogenomics.

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Bradley Martin's Projects

acamel-cookiecutter

cookiecutter template for consistency with directory structure among analyses

acamel_filemanager

Automated system to manage acamel project analyses.

arcgis

Scripts for processing arcGIS files.

bash_scripts

Random bash scripts for working on the AHPCC cluster and for processing input and output files for various programs

btmartin721

clinehelpr

Detects Outliers and plots genomic clines from BGC output, and extends the plotting functionality of INTROGRESS to Correlate genomic clines and hybrid indices with Environmental Variables

construct_pipeline

Pipeline for running conStruct on a distributed HPC system

coordinate_converter

Used to convert GPS coordinates from one format to another.

ddrad_scripts

Random scripts for dealing with ddRAD data, including output from pyRAD

ddradseqtools

dfoil_hdf5

DFOIL: Introgression Testing for Five Taxa

file_converters

File conversion scripts for DNA sequence data

fileman

Research project file manager

fspts

gtseq_pipeline

Pipeline to run GTSeq data through an analytical pipeline.

hzarloop

A python based extension to the HZAR R package, which allow for massively parallel cline fitting. Scalable to potentially 1000's of cpu's for faster data analysis.

locator

deep learning prediction of geographic location from individual genome sequences

makepopmap

Python script to add population identifiers to STRUCTURE, PLINK, and PHYLIP files

mecr_boxturtle

Collection of scripts for doing and plotting machine learning species delimitation results

parallelmrbayes

Runs MrBayes on multiple loci in parallel

parseltongue

pbs_scripts

Some PBS scripts I used to submit my jobs to the University of Arkansas's HPC cluster

pg-sui

Python machine learining API to impute missing genotypes from population genomic data

phylip2eigenstrat

Python script to generate .snp and .ind Eigenstrat files from a PHYLIP infile

pyfuncs

Python functions that I commonly use.

r_scripts

Scripts written in R

radseq

Python scripts for parsing/analyses of RAD-seq data

raxml_ascbias

Script for removing or counting invariant sites for the RAxML ascertainment bias corrections

sapperblarioguys

This game is very incomplete. I hope to work on it more at some point.

scripts

Random scripts, mostly for dealing with RADseq data and DNA sequence alignments

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