shannonekj Goto Github PK

2016-adv-begin-shell-genomics

Workshop content for http://dib-training.readthedocs.org/en/pub/2016-01-13-adv-beg-shell.html

2016-metagenomics-sio

Metagenomics workshop at Scripps Institute of Oceanography

2018-dec-genome-assembly

2018-Dec-Genome-Assembly

2020-ggg-298-first-day-rnaseq

2020-workflows-paper

Strategies for leveraging workflow systems to streamline large-scale biological analyses

2020_ggg298_variant_calling

2021-ggg298-week7

How to use GitHub for GGG298

2021-ggg298-week7-1

Week 7 of GGG 298 at UC Davis, example repository

2021_ggg298_variant_calling

angus

Materials for Analyzing Next-Generation Sequencing (ANGUS) course.

assemblathon2-analysis

collection of scripts and commands used by Ian Korf, Keith Bradnam, and Joe Fass in the analysis of Assemblathon 2 entries (assemblies)

cluster_computing

Tutorials and information on how to approach doing science on compute clusters.

data_organization_and_management

difcover

The DifCover pipeline aims to identify regions in a reference genome for which the read coverage of a sample1 to the reference is significantly different from the read coverage of a sample2. “Significantly different” is determined by user defined threshold on a ration between average coverages of given samples. The pipeline allows to exclude fr

dissertation

ughhhhhh

ds_history_project

ds_ne

Analysis for determining effective population size on historical dataset of delta smelt.

ds_sex-marker

Code related to the identification of sex specific markers in Delta Smelt

farm-notes

notes on the farm cluster

gbs-miscall-rates

estimating genotyping error rates in GBS data using departures from HWE

genome_assembly

Pipeline for genome assembly of eukaryotic organisms...hopefully.

ggradar

radar charts with ggplot2

gvl_bestpractices

Repository for resources and information for working on the command line and cluster.

job_applications

khmer

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

mapping_pipeline

Mapping pipeline for data generated using Arima-HiC

markdown-here

Google Chrome, Firefox, and Thunderbird extension that lets you write email in Markdown and render it before sending.

mhg

scripts related to milk, health and genetics project

mills_rotation

ngs_scripts

scripts I use a lot