Taylor Reiter's repositories
2022-infant-mge
demo workflow to detect mobile genetic elements in metagenomes
2020-paper-sourmash-gather
Here we describe an extension of MinHash that permits accurate compositional analysis of metagenomes with low memory and disk requirements.
2021-sgc-domset-viz
Visualizing dominating sets from spacegraphcats
2022-cf-sputum
Analysis of cystic fibrosis sputum RNA-seq samples for discovery of interesting gene expression pathways
2022-microberna
A pipeline to generate a compendia of bacterial and archaeal RNA-seq data
2022-refinebio-unmapped
Code to explore the unquantified fractions of refine.bio RNA-seq data sets
2022-seqADAGE-pa-model
Building ADAGE models using Pseudomonas aeruginosa RNA-seq data. See https://github.com/georgiadoing/seqADAGE for initial work on this application, and https://bitbucket.org/greenelab/eadage/src/master/ for original eADAGE code
2022-sra-gather
Classify all the metagenomes. ALL THE METAGENOMES. (Eventually.)
2022-test-sketch-core-accessory-interactome
Determine whether some of the results genereated in greenelab/core-accessory-interactome can be regenerated using abundance-weighted FracMinHash sketches instead of gene counts
2023-hackathon-practice
A repository to practice making forks, branches, and pull requests for the Arcadia hackathon.
ADAGEpath
An R package (ADAGEpath) to perform signature analysis using methodology from the ADAGE manuscript
greenelab.com
The website source code for greenelab.com
microberna-manuscript
Manubot manuscript accompanying greenelab/2022-microberna
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
pa-seq-compendia
To build compendia of publicly available RNA-seq data for P. aeruginosa, specifically.
spacegraphcats-dory-example
An example spacegraphcats project!
stamps2022-binder
pangeo binder for use in MBL STAMPS 2022 tutorials
taylorreiter.github.io
blog repo