Codes to simulate data and apply "state-of-art" approaches for integrative analyses between microbiome and metabolome data

R-package for elastic net regularized regression with zero sum constraint

SRA Tools

Genome assembly evaluation tool

Annotate sequences from BLAST against KEGG DB with KO numbers and summarize them in KEGG modules.

A way to extract specific information from CAZy

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

🔎 💊 Mass screening of contigs for antimicrobial and virulence genes

Phylogenetic and taxonomic analysis for genomes and metagenomes

k-mer based Pipeline to identify the Serotype from Illumina NGS reads

❗ This is a read-only mirror of the CRAN R package repository. explor — Interactive Interfaces for Results Exploration. Homepage: https://juba.github.io/explor/ Report bugs for this package: https:…

GeneValidator: Identify problems with predicted genes

Personal VIM configuration, plugins and themes

Statistical Analysis of Metagenomic Profiles

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. …

A general-purpose tool for dynamic report generation in R

Classifier for metagenomic sequences

Ultra-fast and memory-efficient (meta-)genome assembler

An ultra light YAML-based pipeline execution engine

Accelerated BLAST compatible local sequence aligner.

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

An analysis and visualization platform for 'omics data