Projects | Open Source Science

Projects

Scientific Software

Updated 9 months ago

microViz — Peer-reviewed • Rank 4.9 • Science 93%

microViz: an R package for microbiome data visualization and statistics - Published in JOSS (2021)

microbiome microbiome-analysis microbiota r rstats

Engineering Biology (40%)

Scientific Software · Peer-reviewed

Updated 9 months ago

https://github.com/cafferychen777/ggpicrust2 • Rank 13.8 • Science 49%

Make Picrust2 Output Analysis and Visualization Easier

16s-rrna bioinformatics data-visualization differential-abundance functional-data functional-prediction ggplot2 gut-microbiome kegg metagenomic-analysis metagenomics microbiome microbiota pathway-analysis phyloseq picrust2 r r-package tax4fun2 visualization

Updated 9 months ago

micom • Rank 13.3 • Science 39%

Python package to study microbial communities using metabolic modeling.

biochemistry cobra cobrapy community flux hacktoberfest metabolic-models microbiome microbiota modeling python systems-biology

Updated 8 months ago

https://github.com/erictleung/phyloseq-cheatsheet • Rank 1.8 • Science 13%

:notebook: Minimal cheatsheet for functions in the phyloseq R package

bioconductor bioinformatics cheatsheet data-analysis microbiome microbiota notes phyloseq r

Updated 9 months ago

etbf_fbr_stromal_bulkseq • Science 75%

Bulk RNAseq analysis of stromal cells from peri-implant fibrosis of mice with and without ETBF infection

bulk-rna-seq fibrosis manuscript microbiota reproducibility

Updated 9 months ago

vsearchpipeline • Science 44%

VSEARCH pipeline for ASV inference of 16S seq data

16s-seq microbiota vsearch

Updated 9 months ago

https://github.com/barbarahelena/rodam • Science 26%

Analyses Pros-RODAM microbiota data

16s machine-learning microbiota xgboost