Table 2 Temporal omic data software, libraries and packages, tools and web resources ranged from fundamental data preprocessing, immediate analysis to advanced network and pathway and integration analysis
From: Computational dynamic approaches for temporal omics data with applications to systems medicine
Software | Omics variety data, formats | Features/Functions/packages | Web links |
|---|---|---|---|
SAS/JMP Genomics | Various types of genomic data from case-control, SNPs, RNA seq… | Quality-control tools including batch effect removal, PCA, ANOVA, differential analysis, cluster, and prediction e.g., Grinn, MetaMapR, glasso, qpgraph | https://www.jmp.com/en_us/software/data-analysis-software.html |
Matlab | Gene-expression, exon-expression, proteins | Neural network, math optimization modeling, nonlinear dynamic systems; prediction,Multidimensional data visualization, Statistical/machine | |
Bioconductors R | All types of omics data, More than 1200 packages, annotation, experiments, explore, analyze, visualize, | Quality assurance analysis, normalizationVarious statistical (including Bayesian modeling) and algorithm based tools, Cloud-enabled | |
Qlucore Omics Explorer Genedata Expressionist® | RNA seq, microarray, miRNA, Methylation, MS for proteins and metabolites, and Flow cytometry data | Visualization, and biological interpretation; view on the chromatograms; Integration with proteomic and metabolomic data, Automated quality and pre-processing, Standardized workflows | |
DNASTAR GENOSTAR | Exon gene level Microarray, NGS, Protein, RNA-Seq, SNP Metagnomics, chip to chip | Visualizing and Comparing, Multiple Genome-Scale Assemblies modelling and simulation of regulatory networks Automated annotation. | |
iPathwayGuide | miRNA Activity, Molecule interactions DNA proteins interactions | Topology-based Analysis Advanced Correction Factors Prediction, Downstream Impact Analysis Meta Analysis | Advaita Bioinformatics: |
iBioguide | Genes, microRNAs, pathways, biological processes, molecular functions, cellular components, drugs, diseases, | find related genes, pathways, biological processes, molecular functions, cellular components, drugs, diseases, | |
iVariantGuide Genotyping™ Console Software Clinical Genome nClinGen/ClinVar) Rosetta | SNP, copy number variation, SNP genotyping, indel detection | Analyze rare and common variants Genotyping calls, loss of heterozygosity; Dynamic Graphic Filters Pathway Analysis GO Terms Analysis Cloud-based Sharing, Data management and a data repository | https://genegrid.genomatix.com/grid/home. https://www.clinicalgenome.org/tools/webresources/clinician cross-technology/platform analyses |
The Rat Genome Database pathway diagrams | Molecular and physiological pathway; e.g., identifying up or down regulated genes in pathways, see how pathways relate to each other | Pathway acquisition and visualization, multi-layered approach, dynamic and integrated manner, interactive diagram | |
Biotique | Next Generation Sequencing Data, XRAY or other expression, FASTA, FASTQ | Excel plug-in interfaces, Integrated annotations, Illumina Genome Analyzer Pipeline | http://www.biotiquesystems.com/Products-Solutions/GenePress- Solutions/GenePress |