Pinned Repositories
amr_one_health_2021
One Health Summer Institute's Introduction to Bioinformatics workshop. Session on Bioinformatics for AMR Research.
amrplusplus-shiny
Statistical analyses for outputs of the AMR++ analytic pipeline
beebiome-data-portal
A resource for scientists and the general public on bee-associated microbes/viruses and their impact on bee health
bohra
A pipeline for bioinformatics analysis of bacterial genomes
enteroComp
Analysis of Enterococcus AST profiles and marker genes
FluMatch
Automating Prokka annotations, BLAST runs and generation of BLAST reports
impact_of_sequencing_depth
Code for data analysis of the paper "Impact of sequencing depth on the characterization of the microbiome and resistome" by Zaheer et al. (2018)
one_health_continuum
:cow: :pill: :cow2: :poop: Code for the paper Comparative diversity of microbiomes and resistomes in beef feedlots, downstream environments and urban sewage influent.
WGS
Tutorials and resources for bacterial whole genome sequence analysis based on Next Generation Sequencing data
ropolomx's Repositories
ropolomx/amr_one_health_2021
One Health Summer Institute's Introduction to Bioinformatics workshop. Session on Bioinformatics for AMR Research.
ropolomx/taxonomic_profiling_pipeline
ropolomx/beebiome-data-portal
A resource for scientists and the general public on bee-associated microbes/viruses and their impact on bee health
ropolomx/enteroComp
Analysis of Enterococcus AST profiles and marker genes
ropolomx/amrplusplus_v2
MEGARes and AmrPlusPlus - A comprehensive database of antimicrobial resistance genes and user-friendly pipeline for analysis of high-throughput sequencing data
ropolomx/beebiome-taxonomy-scripts
ropolomx/boa-wgs
A Snakemake workflow for the analysis of bacterial WGS data
ropolomx/bothie
ropolomx/dada2_drake_workflow
ropolomx/FIELDimageR-Workshop-11
Workshop presented for NDSU Breeding Pipeline Database Managers. In this course, I went through the basic steps of the FIELDimageR pipeline showing how to evaluate and apply remote sensing data in plant breeding.
ropolomx/fishualize
The fishualize package provides color scales for plotting in R based on nature’s most stunning and colorful organisms: teleost fishes (with a few chondrichthyan cameos).
ropolomx/introduction_to_bioinformatics_wgs
Workshop for introduction to bioinformatics and whole genome sequence analysis
ropolomx/mag
Assembly and binning of metagenomes
ropolomx/metagenomics_rarefaction
ropolomx/metagenote
ropolomx/pea_root_rot
ropolomx/Physalia_ML
ropolomx/pipeline-v5
This repository contains all CWL descriptions of the MGnify pipeline version 5.0.
ropolomx/qiime2R
Import qiime2 artifacts to R
ropolomx/rna-seq-star-deseq2
RNA-seq workflow using STAR and DESeq2
ropolomx/ropolomx
Config files for my GitHub profile.
ropolomx/snakefiles
Snakefiles for reproducible analyses
ropolomx/snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
ropolomx/source_attribution
Produce visualizations using R for source attribution analysis
ropolomx/strategie-devops-strategy
Stratégie DevOps - DevOps Strategy
ropolomx/tan_spot
ropolomx/tourmaline
Amplicon sequence processing workflow using QIIME 2 and Snakemake.
ropolomx/training-material
A collection of Galaxy-related training material
ropolomx/tripal-crop-docker
A fully provisioned Tripal site aimed at supporting crop-focused and breeding research.
ropolomx/WP2_workshop_tool_packaging