emmadebayos Goto Github PK

brassica_genetic_map_paper

calc_allelefrequency_tetraploid

Calculate allele frequencies from a VCF file of tetraploid genotypes

camsa

CAMSA: a tool for Comparative Analysis and Merging of Scaffold Assemblies

clusterflow

A pipelining tool to automate and standardise bioinformatics analyses on cluster environments.

cmplot

📊 Circular and Rectangular Manhattan Plot

community_software_tools_for_ngs

compgenws

Data and scripts for Week 12 in class exercises

count_total_snp_per_population

Want to count how much SNP each of your population have. You are in the right place

cuff_diff_2_xiao_score

Implementation of Xiao., Y. 2014. A novel significance score for gene selection and ranking.

cuffdiff2edger

Perl Script to convert CUFFDIFF output for use with edgeR and Trinity DE analysis

cwl

CWL workflows

datacarpentry.github.io

Data Carpentry website

dismiss-galaxy

DISMISS is an R script, which as an additional step in MeDIP-Seq data analysis workflow, enables the allocation of strands to methylated DNA regions. It does this by analyzing the proportions of first mate reads aligning to the methylated locus from the plus and minus strands.

doc-annovar

Documentation for the ANNOVAR software

easysfs

Effective selection of population size projection for construction of the site frequency spectrum. Convert VCF to dadi/fastsimcoal style SFS for demographic analysis

edirectcookbook

freebayes

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

gaas

Genome Assembly and Annotation Service code

gatk-docs

Documentation archive for GATK tools and workflows

gatk-snp-calling

Full GATK SNP calling pipeline

gatk3-4-rnaseq-germline-snps-indels

Workflows for processing RNA data for germline short variant discovery with GATK (v3+v4) and related tools

genome-scripts

Genome Scripts used in fungal comparative genomics

genomescope2.0

Reference-free profiling of polyploid genomes

genomicconsensus

PacBio® variant and consensus caller

genomics-r-intro

Intro to R and RStudio for Genomics

genomics-workshop

Workshop on Genomics using Palmetto Cluster

germinate-daim

Germinate Daim is a Java based desktop application to aid in the upload of experimental datasets into Germinate.

gwas-polypilene

Pipeline for GWAS in tetraploids

haplotypetools

A toolkit for identifying recombination and recombinant genotypes

humbug-electron

Humbug is a multi-platform barcode generator which can be used alongside our Germinate Scan application to generate sheets of user-defined barcodes to aid in the recording of data in the field or glasshouse.