cypayne Goto Github PK

bbmap

(Not Offical) BBMap short read aligner, and other bioinformatic tools.

cipres-notebooks

SDSC CIPRES Jupyter notebooks for phylo tools

cipres_scripts

Scripts useful for processing input/output files related to CIPRES activities

cypayne.github.io

fastastic

Prokaryotic genome assembly, annotation, + quality check

git-novice

Software Carpentry introduction to Git for novices.

gtseq-scripts

Scripts written to streamline Palumbi lab multiplexing data analysis, which uses the GTseq-Pipeline to produce genotypes (https://github.com/GTseq/GTseq-Pipeline#gtseq-pipeline).

jese4sci-fp

Final Project track of the jese4sci short course

jese4sci.instructors

Instructor material for the jese4sci course

lab_shared_scripts

mega-non-model-wgs-snakeflow

mitonucabc

Uses an ABC framework to estimate selection coefficients against mitonuclear incompatibilities by simulating admixed populations.

ncase_pipeline

openbydesign

A guide to doing open and reproducible science at Stanford

palumbi_scripts

Random scripts used to process data in the Palumbi lab @hopkinsmarinestation http://palumbi.stanford.edu/

qtlmapping_ctmax

Contains QTL mapping pipeline used to map CTmax QTL in Xiphophorus F2s in Payne et al 2021.

shell-novice

Software Carpentry introduction to the shell for novices.

swordtail-offspring-size

Scripts and data for generating figures that appear in Payne et al 2023, "Recent evolution of large offspring size and post-fertilization nutrient provisioning in swordtails"

thermotolerance

Scripts used for QTL mapping, differential gene expression, WGCNA coexpression, etc analyses in Payne et al 2021.

thermtol_wgcna

Pipeline to create gene co-expression networks with WGCNA, run GO enrichment, and permute expected distributions of genes with F1 misexpression from RNAseq data.

trout_scripts