Functional genomics Tools

Enrich2 is a general software tool for processing, analyzing, and visualizing data from deep mutational scanning experiments.

A comprehensive package for performing gene set enrichment analysis in Python.

HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?”

A database which integrates together predictive information about proteins' function from a number of partner resources, giving an overview of the families that a protein belongs to and the domains and sites it contains. Users who have novel nucleotide or protein sequences that they wish to functionally characterise can use the software package InterProScan to run the scanning algorithms from the InterPro database in an integrated way. Sequences are submitted in FASTA format. Matches are then calculated against all of the required member database's signatures and the results are then output in a variety of formats.

New analysis pipeline for Ribosome Profiling (Ribo-seq) experiments, which exploits the triplet periodicity of ribosomal footprints to call translated regions.

ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, hs1 (T2T-CHM13) as well as mouse, worm, fly, yeast, SARS-CoV-2, and many others).

Sequential regulatory activity predictions with deep convolutional neural networks.

Cooler is a support library for a storage format, also called cooler, used to store genomic interaction data of any size, such as Hi-C contact matrices.