ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis
ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data. It is designed to be user-friendly, and has been opt...1562 days ago
1512 days ago
Dahak: benchmarking and containerization of tools for analysis of complex non-clinical metagenomes.
...tegrates state-of-the-art open source tools for metagenomic analyses. Tools in the dahak software suite will perform various steps in metagenomic analysis workflows including data pre-...1540 days ago
ShinyGO v0.61: Gene Ontology Enrichment Analysis + more
2/3/2020: Now published by Bioinformatics. 11/3/2019: V 0.61, Improve graphical visualization (thanks to reviewers). Interactive networks and much more. 5/20/2019...1485 days ago
sunbeam: A robust, extensible metagenomics pipeline
Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. It uses conda to manage dependencies,...1470 days ago
wgd—simple command line tools for the analysis of ancient whole-genome duplications
...to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and colinearity analysis workflows together with tools...1435 days ago
PyParanoid: a pipeline for rapid identification of homologous gene families in a set of genomes
PyParanoid is a pipeline for rapid identification of homologous gene families in a set of genomes - a central task of any comparative genomics analysis. The "gold standard" for identif...1414 days ago
1414 days ago
SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis
...iny application for differential analysis of metagenomic data (16S, 18S...rgeted metagenomics, statistical analysis and results visualization wit...t [Wescott 2015].The statistical analysis is based on DESeq2 R package...standard formats for metagenomic analysis (.csv, .tsv, .biom) and figur...1410 days ago
SqueezeMeta: a fully automated metagenomics pipeline, from reads to bins
SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. SqueezeMeta includes multi-metagenome support allowing the co-assembl...1410 days ago