SchlossLab/snakemake_cluster_tutorial

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SchlossLab/snakemake_cluster_tutorial

SchlossLab

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Brief tutorial for using Snakemake to create and submit jobs on a HPC cluster.

MiSeq_WetLab_SOP

mikropml

User-Friendly R Package for Supervised Machine Learning Pipelines

schtools

Schloss Lab Tools for Reproducible Microbiome Research 💩

Topcuoglu_ML_mBio_2020

Best practices for applying machine learning to bacterial 16S rRNA gene sequencing data

Great_Lakes_SLURM

Using the Great Lakes cluster and batch computing with SLURM

Baxter_glne007Modeling_GenomeMed_2015

Microbiota-based model improves the sensitivity for detecting colonic lesions

Sze_Obesity_mBio_2016

mikropml-snakemake-workflow

Snakemake template for building reusable and scalable machine learning pipelines with mikropml

Hannigan_CRCVirome_mBio_2018

Investigating the gut virus communities associated with colon cancer.

Kozich_MiSeqSOP_AEM_2013

Reproducible analysis of sequence analysis on a MiSeq

ipython-mothurmagic

IPython extension for running mothur commands in an IPython notebook

Jupyter Notebook

Schloss_rrnAnalysis_mSphere_2021

Code Club project analyzing utility of ASVs

schlosslab.github.io

The website for the Schloss Lab at the University of Michigan

Schloss_PacBio16S_PeerJ_2016

Repo for Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

Sze_CRCMetaAnalysis_mBio_2018

Schloss_PacBio16S_PeerJ_2015

Repository to accompany "Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system"

Jenior_Metatranscriptomics_mSphere_2018

Repository associated with Jenior ML, et al. (2018). mSphere.

intro-testing-r

Introduction to Testing R Code

Zackular_AbAOMDSS_mSphere_2015

Repository to accompany "Manipulation of the Gut Microbiome Reveals Role for Microbial Community Structure in Colon Tumorigenesis"

Schloss_Singletons_XXXXX_2023

Stough_Mouse_RNA_Virome_MRA_2019

Schloss_Cluster_PeerJ_2015

Replication study of He et al. (2015) in Microbiome by Pat Schloss & Sarah Westcott

mothur-snakemake-workflow

Snakemake template for microbial amplicon sequence analysis with mothur.

Baxter_WildMice_AEM_2014

R notebook describing data analysis for "Intra- and inter-individual variation masks inter-species variation in the microbiota of sympatric Peromyscus populations"

FusoAssemblies

Pipeline for assembling Fuso genomes from HMP shotgun sequences

documenting-R

Materials for a code review on documenting R code.

Doherty_CDprediction_mBio_2017

repo for the paper

Flynn_LRColon_CancPrevRes_2017

Kaitlin's repo for the LR KWS colon project

Schloss_Rarefaction_mSphere_2024

Westcott_OptiClust_mSphere_2017

Paper describing opticlust method published in mSphere

Schubert_AbxD01_mBio_2015

Reproducible workflow for Schubert et al. 2015 mBio

Sovacool_OptiFit_mSphere_2022

The manuscript accompanying the OptiFit algorithm in mothur

Sze_PCRSeqEffects_mSphere_2019

The impact of DNA polymerase and number of rounds of amplification in PCR on 16S rRNA gene sequence data

Tomkovich_PEG3350_mSphere_2021

Hannigan_ConjunctisViribus_ploscompbio_2018

Using graph database techniques to understand the infectious relationships between bacteria and phages.

Hagan_CodeClub_PLOSComp

Repository for collaboratively written 10 Simple Rules to Code Clubs paper

Armour_Resolution_mBio_2021

Analysis of optimal taxonomic resolution for predicting SRNs from microbiome data

bipartite_graphs

Lesniak_Severity_mBio_2022

severe-CDI

Predicting CDI severity from OTUs

Lesniak_Clearance_mSphere_2021

Effect of C. difficile colonization on recovery of gut microbiota in antibiotic-treated mice

Schloss_WNWN_mSphere_2023

Baxter_FITs_Microbiome_2016

opf

Scripts and tutorials for creating opfs from metagenomic data

pdsBayesian

just-enough-python

Just enough Python for R users to write advanced Snakemake workflows

vscode-code-club

Code club to introduce VS Code

Sze_FollowUps_Microbiome_2017

Schloss_PrePrints_mBio_2017

Schloss_IonTorrent_2015

Repository to analyze 2015 IonTorrent 16S rRNA gene sequence data quality

Code_Review_42717

Adonis Code Review

gol

What the Package Does (One Line, Title Case)

Jenior_Modeling_mSystems_2017

Repo associated with Jenior et. al. (2017). Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes. mSystems.