mSFS using a teosinte natural population

Rescale genetic polymorphism data to match a common sample size.

Successful Job Applications and Grants

A data science IDE for Python

Cutadapt removes adapter sequences from sequencing reads

deepstream.io server

JupyterLab computational environment.

DeepDive

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

Specifications of SAM/BAM and related high-throughput sequencing file formats

Impute GBS genotype

Using ANGSD and Python/R to calculate and plot pi-between in windows along the genome

Generic pipeline system

R's data.table package extends data.frame:

Programs to analyse NGS data for population genetics purposes

An interactive data visualization tool which brings matplotlib graphics to the browser using D3.

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtool…

🔬 Assemble large genomes using short reads

De novo transcriptome assembler for short reads

A fast and sensitive gapped read aligner

An ultrafast memory-efficient short read aligner

Transcript database for Zea mays Ensembl AGPv2.17

Tools for bioinformatics moved to http://git.genenetwork.org/pjotrp/bioinformatics

A command-line power tool for Twitter.

An sklearn-like python package for pegasos models

Example R scripts and data for "Practical Data Science with R" 1st edition by Nina Zumel and John Mount (Manning Publications)

Code accompanying the book "Machine Learning for Hackers"

Example code for running R on Hadoop

Very concise notes on machine learning and statistics.

📙 The probability and statistics cookbook