Tools for Human Data

methylKit - R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing
metilene: Differential methylation
MOFA - versatile and statistically rigorous generalization of PCA to multi-omics data
muvac: Variant calling pipeline
NGLess - domain-specific language for next-generation sequencing data processing
OmniPath - database of causal protein-protein interactions
OpenPepXL - Protein-Protein cross-linking tool
OTP - comprehensive framework for NGS project organization and processing
PAA - R/Bioconductor package for protein microarray data analysis
PanCancer alignment workflow
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
PRECOG - predict GPCR-G-protein couplings
proGenomes - consistent taxonomic and functional annotations for bacterial and archaeal genomes
PROGENy - infer pathway activity from gene expression
ProteomicsLFQ - Large scale analysis workflow for label free analysis
PUBLISSO - open access publishing platform for research articles
rGREAT - Automatic Genomic Regions Enrichment of Annotations Tool (GREAT)
rhdf5 / Rhdf5lib - an interface between HDF5 and R