Data

Tools

Indexes

Applications

Experiments

Awesome

An open API service indexing awesome lists of open source software.

Projects in Awesome Lists by SchlossLab

A curated list of projects in awesome lists by SchlossLab .

https://github.com/SchlossLab/mikropml

User-Friendly R Package for Supervised Machine Learning Pipelines

machine-learning r-package rstats

Last synced: 13 Jul 2025

https://github.com/schlosslab/great_lakes_slurm

Using the Great Lakes cluster and batch computing with SLURM

batch-computing hpc slurm

Last synced: 28 Feb 2026

https://github.com/schlosslab/mikropml-snakemake-workflow

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

machine-learning rstats snakemake

Last synced: 30 Oct 2025

https://github.com/schlosslab/ipython-mothurmagic

IPython extension for running mothur commands in an IPython notebook

Last synced: 30 Oct 2025

https://github.com/schlosslab/snakemake_cluster_tutorial

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

Last synced: 30 Oct 2025

https://github.com/schlosslab/schloss_rrnanalysis_msphere_2021

Code Club project analyzing utility of ASVs

Last synced: 30 Oct 2025

https://github.com/schlosslab/schloss_pacbio16s_peerj_2016

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

reproducible-paper

Last synced: 24 Feb 2026

https://github.com/schlosslab/zackular_abaomdss_msphere_2015

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

reproducible-paper

Last synced: 30 Oct 2025

https://github.com/schlosslab/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"

reproducible-paper

Last synced: 25 Feb 2026

https://github.com/schlosslab/westcott_opticlust_msphere_2017

Paper describing opticlust method published in mSphere

reproducible-paper

Last synced: 23 Feb 2026

https://github.com/schlosslab/mothur-snakemake-workflow

Snakemake template for microbial amplicon sequence analysis with mothur.

16s-rrna mothur snakemake

Last synced: 30 Oct 2025

https://github.com/schlosslab/schloss_cluster_peerj_2015

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

reproducible-paper

Last synced: 25 Feb 2026

https://github.com/schlosslab/severe-cdi

Predicting CDI severity from OTUs

Last synced: 30 Oct 2025

https://github.com/schlosslab/hannigan_conjunctisviribus_ploscompbio_2018

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

bacteria microbiome phage phage-bacteria-networks reproducible-paper

Last synced: 23 Feb 2026

https://github.com/schlosslab/hagan_codeclub_ploscomp

Repository for collaboratively written 10 Simple Rules to Code Clubs paper

Last synced: 23 Feb 2026

https://github.com/schlosslab/schubert_abxd01_mbio_2015

Reproducible workflow for Schubert et al. 2015 mBio

reproducible-paper

Last synced: 30 Oct 2025

https://github.com/schlosslab/fusoassemblies

Pipeline for assembling Fuso genomes from HMP shotgun sequences

Last synced: 26 Feb 2026

https://github.com/schlosslab/lesniak_clearance_msphere_2021

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

Last synced: 30 Oct 2025

https://github.com/schlosslab/schloss_iontorrent_2015

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

Last synced: 26 Feb 2026

https://github.com/schlosslab/just-enough-python

Just enough Python for R users to write advanced Snakemake workflows

code-club python quarto rstats snakemake tutorial

Last synced: 16 Apr 2026

https://github.com/schlosslab/vscode-code-club

Code club to introduce VS Code

code-club

Last synced: 30 Oct 2025

https://github.com/schlosslab/code_review_42717

Adonis Code Review

Last synced: 30 Oct 2025

https://github.com/schlosslab/opf

Scripts and tutorials for creating opfs from metagenomic data

Last synced: 30 Oct 2025

https://github.com/schlosslab/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.

reproducible-paper

Last synced: 30 Oct 2025

https://github.com/schlosslab/tidy-eval

A brief introduction to tidy evaluation

code-club tidy-eval tidyverse

Last synced: 22 Feb 2026

https://github.com/schlosslab/gildedrose

Inventory for the Gilded Rose

Last synced: 30 Oct 2025

https://github.com/schlosslab/fit-tests

Test to see if DNA isolated from FIT tests can be used as a surrogate for stool

Last synced: 24 Feb 2026

https://github.com/schlosslab/pds_dmm

Command line tool to calculate Laplace fit values for user supplied community type assignments

Last synced: 30 Oct 2025

https://github.com/schlosslab/2019-12-02-close_codereview_rsubsamplingshared

Review of Will Close's code for subsampling shared files to a desired number of reads.

Last synced: 30 Oct 2025

https://github.com/schlosslab/armour_optifitglne_msphere_2023

Application of the OptiFit algorithm to CRC dataset to predict SRNs from microbiome data

Last synced: 30 Oct 2025

https://github.com/schlosslab/ding_hmp_nature_2014

IPython notebook that accompanied Ding & Schloss 2014 paper in Nature

reproducible-paper

Last synced: 30 Oct 2025

https://github.com/schlosslab/quarto_code_club

Introduction to Using Quarto

Last synced: 25 Feb 2026

https://github.com/schlosslab/plot-recreation

Re-creating plots to learn cool tricks and practice problem-solving.

code-club data-viz tidyverse

Last synced: 22 Feb 2026

https://github.com/schlosslab/schubert_clinical_mbio_2014

Repository for Schubert et al. 2014 published in mBio

reproducible-paper

Last synced: 23 Feb 2026

https://github.com/schlosslab/schloss_census2_mbio_2016

Update of the 2004 Schloss & Handelsman MMBR paper "Status of the Microbial Census"

reproducible-paper

Last synced: 23 Feb 2026

https://github.com/schlosslab/colovas_data_accessibility

New repository for Data Accessibility project begun by Adena Collens.

schlosslab-greatlakes schlosslab-papers-wip schlosslab-r

Last synced: 24 Feb 2026

https://github.com/schlosslab/logos

The lab's hex logos combined in one image

Last synced: 25 Feb 2026

https://github.com/schlosslab/outlining_tutorial

Example of how to develop outlines and convert them to papers

schloss-tutorial schloss-writing

Last synced: 26 Feb 2026

https://github.com/schlosslab/schloss_reprocomment_mbio_2018

Commentary on reproducible research in microbiology

Last synced: 26 Feb 2026

https://github.com/schlosslab/nlrp6_analysis

Mothur analysis of colonization of GF WT and Nlrp6 KO mice

Last synced: 26 Feb 2026