Shawn Higdon's repositories
R-t2d-deseq2-phyloseq
Analysis of metatranscriptome data from human microbiomes using phyloseq and deseq2
snakemake_lactococcus
analytical pipeline for lactococcus isolate genomes
bcw-lactococcus-shell
A repository containing shell scripts used to analyze L. lactis WGS data on an hpc with SLURM
bin-bam-boom
extract fastq reads from bam files
R-Mucilage-isolate-pgp-assay
R Analysis of phenotypic assay data screening mucilage isolates for plant growth promotion traits
R-Mucilage-isolate-pgp-genes
R analysis of hmmscan output from mucilage isolates using models for pgp marker genes
rnaseq-hpc-shell
Shell Scripts used to compute output with rnaseq datasets
shigdon.github.io
:rocket: Repo for Personal Website and Blog
snakemake_mucilage-isolates
snakemake workflow for analysis of microbial isolates from Zea mays
R-alt-nif-analysis
Code for alternative nif Gene mining analysis
R-bcw-lac-analysis
A repository for the R Project containing code to generate L. lactis pangenome analysis figures
R-bionectria-cazymes
Analysis of bionectria genome cazymes in R Studio
R-mmm-dge
Maize mucilage metatranscriptome differential gene expression analysis in R
R-Mucilage-bnf
Analysis of bnf phenotype data for mucilage isolates
R-Mucilage-isolate-potato-inplanta-assay
data analysis of in planta potato mono isolate inoculations
R-Mucilage-isolates-dbCAN2
R Analysis of data output from scanning mucilage isolate genomes using dbCAN2
R-Mucilage-isolates-nif
R analysis of NIFscan output files from mucilage isolates
R-Mucilage-isolates-sourmash
R analysis of Sourmash output using mucilage isolate genome sequences
R-t2d-saliva-deseq2
Differential Expression Analysis of saliva microbiome data with DEseq2
rf-ms3
random forests analysis of L. lactis pan genome data
salty-bugs
Analysis of salt loving microbes
snakemake_meta-rnaseq
A snakemake workflow for the analysis of human metatranscriptome datasets
stag-mwc
StaG Metagenomic Workflow Collaboration