laninsky Goto Github PK

non_active_repos

Repos that are no longer actively maintained

organization-genomics

penguins

Analysis code used for penguin project

phase_everyone

Phase_hybrid... phases hybrids. This phases all the samples in your next-gen dataset

phase_hybrid_from_next_gen

Have you got a hybrid in your ultra-conserved element dataset, and you want to confirm its parent species? Then boy, do I have the pipeline for you!

plotting_functions

Some functions for using R to plot data prettily

polg_mice

Trying to determine the "phase" when multiple heteroplasmic sites are recovered across a mitogenomic sequence

pop-genomics-workshop2019

Content for MAPNET Workshop in analysis of low-coverage population genomic data

possums

Leveraging hybrid zones to identify genes important to reproduction and survival in possums

processing_fastsimcoal_to_fasta

Taking the concatenated arlequin file from fastsimcoal and splitting by locus

project_logs

Log of analyses conducted for various projects

pulling-out-mitogenomes-from-uce-data

General pipeline for skimming mitogenomic data from UCE runs

r-ecology-lesson

:notebook: Data Carpentry R lessons on ecology.

reference_aligning_to_established_loci

From a set of established loci obtained from pyRAD, mapping raw reads for new samples back to these

reference_database_creator

creating reference databases for amplicon sequencing

robin

Analyses related to robin genome paper

ruatau

Web-based resources associated with Ruatau

sfs_workshop

Running through using CubSFS to do demographic reconstructions using an SFS

shell-novice

Software Carpentry introduction to the shell for novices.

shiny_pomonella

Code for shiny plots of pomonella RNAseq and poolseq

snp_comparisons

Calculating numbers of mismatching loci based on structure files

species_occurence

Implementing Simper in an Rscript

sperm_whales

Analysis code used on sperm whale paper

structure_on_the_server

How to get your sweet structure analysis going on a linux server

summarise_alignment_position

Given a phylip alignment file, and assuming the reference is in the top line of the alignment, will calculate the start and stop (both gapped and ungapped) of all other sequences in the alignment relative to the reference

teaching

teaching_resources

Alana Alexander's genomics & tiaki rauemi

tidy-projects

uce_divergence_times

Using pairwise distances between UCE sequences to roughly date the MRCA of ingroup samples

uce_processing_steps

The general workflow for processing UCE data that I use