R toolkit for single cell genomics

🎄Visualization and annotation of phylogenetic trees

A grammar of graphics for comparative genomics

Fast Disk-Based Parallelized Data Manipulation Framework for Larger-than-RAM Data

R package for community ecologists: popular ordination methods, ecological null models & diversity analysis

🌈 Interactive analysis of metagenomics data

Personal Cancer Genome Reporter (PCGR)

Quality control for MinION sequencing data

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks

Julia package for loading many of the data sets available in R

DAS Tool

Testing differences in cell type proportions from single-cell data.

Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2

Somatic copy variant caller (CNV) for next generation sequencing

Locate antiviral defence systems in prokaryotic genomes

Models of the Microbial Pangenome

Fast and pretty dotplots for whole genomes assemblies using minimap2 and R/ggplot2

Kannapedia genomic selection data exploration and analysis