Tools for Human Data

methylKit - R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing
MHCquant - A Workflow for Identification and Quantification of HLA Ligands
MOFA – Multi-Omics Factor Analysis
MuVi - a multi-view latent variable model with domain-informed structured sparsity
NGLess - domain-specific language for next-generation sequencing data processing
OmniPath - database of causal protein-protein interactions
OTP - comprehensive framework for NGS project organization and processing
PanCancer alignment workflow
PATCH - Collection of software solutions for pangenome analyses
PeptideShaker - Proteomics analysis suite for quality control, identification and quantification
PIA - toolbox for MS based protein inference and identification analysis
PiGx - Reproducible workflows for genomics
PLAST - Pangenome Local Alignment Search Tool
proGenomes - consistent taxonomic and functional annotations for bacterial and archaeal genomes
PROGENy - infer pathway activity from gene expression
ProtGraph – Protein Graph Generation from UniProtKB Entries
PUBLISSO - open access publishing platform for research articles
quantMS - OpenMS in the quantMS workflow
rGREAT - Automatic Genomic Regions Enrichment of Annotations Tool (GREAT)
rhdf5 / Rhdf5lib - an interface between HDF5 and R

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