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ragtag

Fast reference-guided genome assembly scaffolding

rgeode

The aim of the RGEOde project was to develop a bioinformatics unit that could be implemented broadly, by not requiring any computer programming experience and using free software and publically-available data. Teaching materials were designed to present the content in a tutorial, interactive fashion that appeals to multiple student learning styles. The lesson sequence builds on gene expression concepts covered in high school biology, reinforcing student comprehension through bioinformatics analysis of gene expression microarray data using the R programming language.

rladies_bmo

RLadies Baltimore Chapter

rnaseq

RNA sequencing analysis pipeline using STAR or HISAT2, with gene counts and quality control

samtools

samtools on Windows x64

shiny_rnaseq

shinyngs

Shiny apps for NGS etc based on reusable components created using Shiny modules

speedseq

A flexible framework for rapid genome analysis and interpretation

svm-r-markdown-templates

I have a suite of R Markdown templates for academic manuscripts, beamer presentations, and syllabi. I share them here.

swigg_shiny

Shiny app for visualizing genome graphs from SWIGG

testrepo

tools4rr

Materials for a one-credit course on reproducible research

tophat

Spliced read mapper for RNA-Seq

traz

vcf-to-23andme

Convert imputed DNA.Land VCF to 23andMe V3 raw data format

warpgroup

The warpgroup algorithm takes multiple LC/MS samples and determines: 1. Segregation of those peaks into compound groups; 2. Per-group consensus integration bounds; 3. Integration bounds for samples in which no peak was detected.

workflowr

Organize your project into a research website