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adaptiphy

This computational method has been published in BMC genomics as: "Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral"

ancestry_voting_for_sea_urchins

These scripts were created to show how we were able to run Ancestry Voting in The Wray-McClay lab to identify developmental trajectories in Sea Urchins. We are extrimely grateful with Jonas Brandenburg who shared his orginal scripts with us.

annotatingtranscriptomes

Assembly and annotation of transcriptomes de novo

assembling_viruses

chipseq

ChIP seq pipelines and launchers

conservation-plotting

Here I used PHAST (phyloFit and PhastConst) to generate conservation scan along the avpr1a locus in prairie voles

genomewide_alignment

I will use Cactus to create a genome wide alignment

miscelaneous

here I post scripts (not necessarily optimal) but do the work

rna-seq

RNAseq analysis: mapping pipelines and launchers

scicomp-oct

Test repo for the SciComp course

single_cell_genomics

wot

A software package for analyzing snapshots of developmental processes