Pinned Repositories
amr-nextflow
A Nextflow-based set of scripts for running the MEG Antimicrobial Resistance AmrPlusPlus pipeline
bear-wgs
USDA ARS BEARRU Whole Genome Sequencing Workflow
cuda-half-testing
cuda-sandbox
Toy examples of CUDA kernels
fast-mle-multinomials
Fast MLE for the Beta-Liouville Multinomial
meta-marc
Metagenomic Markov Models for Antimicrobial Resistance Characterization - Source code
nextflow-singularity-template
A barebones template for Bioinformatics pipelines using Nextflow and Singularity
python-workshop
Notes/Syllabus for the Python Beginner's Workshop
sam-parse-merge
simple-snp
lakinsm's Repositories
lakinsm/meta-marc
Metagenomic Markov Models for Antimicrobial Resistance Characterization - Source code
lakinsm/python-workshop
Notes/Syllabus for the Python Beginner's Workshop
lakinsm/bear-wgs
USDA ARS BEARRU Whole Genome Sequencing Workflow
lakinsm/amrplusplus-shiny
Shiny app for running AMR++ analytic pipeline from the Microbial Ecology Group
lakinsm/csu-sequencing-fall2019
16S Data Analysis for MIP565
lakinsm/meta-marc-publication
Metagenomic Markov Models for Antimicrobial Resistance Characterization - Publication code
lakinsm/cuda-half-testing
lakinsm/fast-mle-multinomials
Fast MLE for the Beta-Liouville Multinomial
lakinsm/nextflow-singularity-template
A barebones template for Bioinformatics pipelines using Nextflow and Singularity
lakinsm/sam-parse-merge
lakinsm/simple-snp
lakinsm/alignment-tools
lakinsm/asffast-container
Singularity container for ASF-FAST
lakinsm/asfv-genomes
African Swine Fever Genomes from ASFV DB
lakinsm/csu-cs-cluster
Scripts for running jobs on the computer science cluster at CSU
lakinsm/csuthesis
Colorado State University LaTeX Thesis/Dissertation Template
lakinsm/erl-mare-microbiome
16S ribosomal DNA characterization of the reproductive tract microbiome in normal and infected Quarter Horse mares
lakinsm/fad-snp-utils
lakinsm/meg-bayesian-regression
Testing Bayesian regression MCMC techniques on resistome/microbiome data
lakinsm/meg_resistome_power_calculation
Power calculation for shotgun metagenomic studies of AMR
lakinsm/mmarc-snp
SNP metadata for the Meta-MARC models
lakinsm/modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
lakinsm/numerical-optimization
lakinsm/slss-asffast
ASF-FAST pipeline for USDA APHIS SLSS
lakinsm/slss-denovo
De novo assembly short/long/hybrid pipeline for the USDA APHIS SLSS section
lakinsm/strep-equi-mra
Publication code for Streptococcus equi MRA submission
lakinsm/summit-assembly
Assembly pipeline for the Boulder Summit HPC cluster
lakinsm/TAW-RLG-REST
RESTful query for TAW RLG Division
lakinsm/Tychus
lakinsm/usda-ars-scripts
USDA ARS BEARRU Miscellaneous Utility Scripts