Projects in Awesome Lists by Snitkin-Lab-Umich
A curated list of projects in awesome lists by Snitkin-Lab-Umich .
https://github.com/snitkin-lab-umich/prewas
R package to perform data pre-processing for more informative bacterial GWAS
bacterial-genomes gwas gwas-tools microbiology r r-package
Last synced: 13 Apr 2025
https://github.com/snitkin-lab-umich/regentrans
regentrans: R package for investigating regional pathogen transmission using genomic data
Last synced: 15 Apr 2025
https://github.com/snitkin-lab-umich/micro582-epi582-winter-2024
MICRO582/EPI582 - Genomic Epidemiology Winter Course 2022
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/qcd
Runs Quality Control workflow on Illumina WGS data
Last synced: 15 Apr 2025
https://github.com/snitkin-lab-umich/genome_downloading_snakemake
Snakemake pipeline to download genomes from NCBI using Biosample Accession Numbers and fasterq-dump
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/prewas_manuscript_analysis
Manuscript in support of prewas software
data data-visualisation manuscript r
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/snitkitr
common R functions used in the lab
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/ml-crkp-infection-manuscript
Code and some data related to manuscript on machine learning to study CRKP colonization and infection
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/caurisblast
Python scripts to assist with BLASTing sequences from Candida auris
Last synced: 28 Mar 2025
https://github.com/snitkin-lab-umich/snakemake_setup
Setup information for snakemake pipelines
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/ltach-crkp-colistin-ms
Data, code, and figures corresponding to LTACH CRKP colistin manuscript
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/funqcd
Quality control pipeline for short read fungal data
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/cauris_dotplot
A set of simple scripts for generating synteny dot plots from C auris assemblies
Last synced: 06 Apr 2025
https://github.com/snitkin-lab-umich/cauris-data-flow
data flow scripts for C auris sequencing
Last synced: 07 Apr 2025
https://github.com/snitkin-lab-umich/nanofunqc
QC and annotation pipeline for C auris nanopore sequencing data
Last synced: 30 Mar 2025
https://github.com/snitkin-lab-umich/nanofunsake
A pipeline for hybrid assembly, QC, and annotation of C auris genomes
Last synced: 10 Mar 2025
https://github.com/snitkin-lab-umich/code_club_curriculum
Curriculum for the Snitkin Lab Code Clubs
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/ariba_snakemake
Snakemake pipeline to run ARIBA on genomes using CARD, PlasmidFinder, or MLST database
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/eip-cre-transmission-ms
Code and data related to EIP CRE transmission project
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/unittestsandfunctionchecks
UnitTestsAndFunctionChecks
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/data-flow-sop
SOPs for processing short, long, and hybrid bacterial data
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/ndm-st147-chicago-ms
Code related to manuscript: Regional spread of blaNDM-1-containing Klebsiella pneumoniae Sequence Type 147 in post-acute care facilities
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/nanoqc
Quality control pipeline for nanopore long read data
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/sample_snakemake
Example snakemake pipeline
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/snpkit-smk
Snakemake workflow for Microbial Variant Calling, Recombination detection and Phylogenetic tree reconstruction.
Last synced: 21 Mar 2025
https://github.com/snitkin-lab-umich/data-carpentry-genomics
Instructor notes for Data Carpentry for genomics 2-day workshop
Last synced: 21 Mar 2025