Here are some software packages developed by my group.
Genomics (RNAseq, search, etc.)
Salmon – fast, accurate isoform abundance estimation from RNA-seq data (spiritualy Sailfish 2.0).
Sailfish – ultrafast isoform abundance estimation from RNA-seq reads.
JELLYFISH – count k-mers in large sequence databases very fast.
Sequence Bloom Trees – search for large raw read collections.
Ribomap – mapping for riboseq reads.
MINCE – reference-free compression of short-read sequencing data.
PathEnc – reference-based compression of short read data sets.
GiRaF – find reassortments in collections of influenza genome sequences.
TransTermHP – find rho-independent transcription terminators in bacterial genomes.
Hi-C & Genome Structure
Armatus – multi-scale topological domain detection from Hi-C data.
STARFISH – Identify rigid components with the pebble game and a body-bar-and-hinge reduction
PARANA 2 – parsimonious estimates of ancestral networks.
CORAL – system for interactive visualizations of differences between clusterings.
PARANA – parsimonious reconstruction of ancestral interaction networks.
GHOST – Global alignment between two graphs.
Network Archaeology – infer evolutionary history of a network.
VI-Cut – find a clustering that best matches imperfectly-known cluster hints.
Map of Jazz Musicians – web application to explore recorded collaborations between jazz musicians.