Table 2:
Selected Bioinformatics/Systems Biology Resources for Multi-Omics Studies.
| Tool | Description | Ref. |
|---|---|---|
| Search | ||
| Eagle2 | Open-source, imputation/haplotype phasing | 178 |
| Bowtie2 | Open-source; sequence alignment to reference genome | 179 |
| SAMtools | Open-source; SNP/variant calling | 180 |
| STAR/HTSeq | Open-source; RNA-seq genome annotation/alignment, read mapping, counting | 181,182 |
| Kallisto/Sailfish/Salmon | Open-source; transcriptome pseudocounts; sample-specific bias models | 183–185 |
| seqcluster | Open-source; miRNA alignment and annotation | 186 |
| Proteome Discoverer | Commercial; protein/peptide sequence ID; label-free, MS1-/isobaric labeling, PTMs | 187 |
| MaxQuant | Free; quantitative shotgun proteomics; label-free, MS1-/isobaric labeling, PTMs | 188 |
| Skyline | Open source; targeted proteomics/metabolomics; selected/multiple/parallel reaction monitoring | 189 |
| Compound Discoverer | Commercial; small-molecule structural identification; visualization; stable isotope labeling (untargeted); metabolite pathway analysis | 190 |
| XCMS Online | Free; untargeted metabolomics; retention time matching; compound ID; multiple reaction monitoring; differential statistics; visualization; integration; metabolite pathway analysis | 191 |
| Cell Ranger | Free; single-cell RNA-seq output processing; read alignment, generation of feature-barcode matrices, clustering, gene expression analysis | 192 |
| Statistical Analysis/Differential Expression | ||
| PLINK | Open source; whole-genome association analyses; linkage disequilibrium; stratification | 193 |
| SNPTest | Free; single SNP association in genome-wide studies; binary and multiple phenotypes; Bayesian and Frequentist tests | 194 |
| FastQTL | Open-source; cis-QTL mapping; beta approximation-based permutation scheme; internal quantile normalization of phenotypes | 195 |
| QTLtools | Open-source; molecular QTL discovery/analysis; sequencing data QC; cis/trans QTL mapping; functional annotation density; QTL enrichment; covariate correction | 196 |
| DESeq2 | Open-source; transcript quantification/differential expression; normalization (median of ratios) | 197 |
| EdgeR | Open-source; transcript quantification/differential expression; normalization (mean of Ms) | 198 |
| Perseus | Free; protein quantification, interaction, PTMs; high-dimensional omics; normalization, time-series, multiple-hypothesis tests; patient classification | 199 |
| MSstats | Open-source; label-free and label-based proteomics; statistical relative quantification; visualization; differential protein abundance | 200 |
| MetaboAnalyst | Free; high-throughput metabolomics; differential metabolite abundance; classification; visualization, compound ID; ontology | 201 |
| Qlucore Omics Explorer | Commercial, multi-omics (RNA-seq, DNA-seq, DNA methylation, single-cell, proteomics, metabolomics, flow); visualization; differential enrichment; clustering | 202 |
| Seurat | Open-source; single-cell; QC/normalization; clustering; dimensionality reduction; differential expression, highly-variable genes; integration; visualization | 203 |
| Monocle | Open-source; single-cell; clustering; dimensionality reduction; differential expression, visualization; time-series/pseudo-time | 140 |
| Loupe Browser | Free; single-cell; filtering, clustering; differential expression; integrated V(D)J and gene expression analysis; visualization | 204 |
| Multi-Omics Integration | ||
| MOFA | Open-source; heterogenous/sparse datasets; bulk/single-cell; latent factors of variation | 174 |
| PaintOmics | Free; transcriptomics/proteomics/metabolomics/ATAC-seq/ChIP-seq; KEGG pathway-based integration; visualization; pathway analysis | 205 |
| Escher | Open-source; genomics/transcriptomics/proteomics/metabolomics; gene/reaction/metabolite pathway visualization |
206 |
| Cross-Species Translation | ||
| sbv IMPROVER | Open-source; crowdsourcing; biological networks; automated literature curation | 136 |
| diseaseQUEST | Open-source; integration of human GWAS and model organism network models of tissue/cell-type-specific function, machine learning, candidate gene prioritization | 137 |
| FIT | Free; cross-species extrapolation of gene expression between mice and humans | 135 |
| Interactions, Ontologies, Networks, and Pathways | ||
| ConsensusPathDB | Molecular function interaction database; gene/metabolite enrichment; multi-level gene ontology and multi-database pathway enrichment; protein interactions; visualization | 207 |
| Enrichr | Gene set enrichment analyses; gene ontology; multi-database pathways; protein complexes; small molecule perturbagens; human phenotypes; tissue/cell type expression; visualization | 208 |
| STRING | Protein-protein interaction networks; functional enrichment analyses; visualization | 209 |
| MetaCore | Commercial; curated; protein-protein/DNA-protein/protein-compound interactions; transcription factors; metabolic/signaling pathway analyses; ontologies; visualization | 210 |
| DAVID | Free; ontology/pathway enrichment; BioCarta & KEGG pathway visualization; protein interaction; gene-disease associations | 211 |
| Cytoscape | Open-source; integration and visualization of multi-omics molecular interaction networks; ontology/pathway enrichment; network analyses; clustering | 212 |
| Ingenuity | Commercial; multi-omics integration, pathway analyses; network visualization/causal analyses | 213 |
| WGCNA | Open-source; network construction, module detection, gene selection, calculation of topological properties, data simulation, visualization | 214 |