Joe Colgan's repositories
bter_population_genomics
Genomics of adaptation to a changing world in a wild bumblebee
sphaerularia_rnaseq
Infection by the castrating parasitic nematode Sphaerularia bombi changes gene expression in Bombus terrestris bumblebee queens
ase
repo for code to implement allele-specific gene expression model of Skelly et al. 2011 Genome Res https://dx.doi.org/10.1101/gr.119784.110
biostat561
Course materials for BIOST561
bombus_mated_worker_analysis
Scripts for the analysis of RNA-seq datasets generated for the manuscript "Unexpected worker mating and colony-founding in a superorganism."
bter_immune_gene_evolution
Signatures of adaptation, constraints, and potential redundancy in the canonical immune genes of a key pollinator
Bter_neonicotinoid_exposure_experiment-1
Caste- and pesticide-specific effects of neonicotinoid pesticide exposure on gene expression in bumblebees
bumblebee_proteomics
Mating precedes selective immune priming which is maintained throughout bumblebee queen diapause.
filter-fastq
Filter reads from a FASTQ file using a list of identifiers.
genotype_plot
A set of functions to visualise genotypes based on a VCF
haplogrep-cmd
HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
Joscolgan
Config files for my GitHub profile.
joscolgan_old_site
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
Learn-Pandas
Tutorials on how to use pandas effectively to do data analysis
MicrobiomeBestPracticeReview
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
OrthoFinder
Phylogenetic orthology inference for comparative genomics
pipeline-transcriptome-de
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
Proteus
R package for analysing proteomics data
r-color-palettes
Comprehensive list of color palettes available in r ❤️🧡💛💚💙💜
Research-Lab-Website
This is a simple static research lab website template which can be used by college students / professors.
rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
salmo_smolt_study
Salmo smoltification RNA-seq study
salmonid_immune_study
Evolution and expression of the immune system of a facultatively anadromous salmonid
SURVIVOR
Toolset for SV simulation, comparison and filtering
time
A NetLogo extension that brings date/time utilities and discrete event scheduling to NetLogo