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

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	http://www.mathworks.com/
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	http://bioconductor.org/
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	www.qlucore.com https://www.genedata.com/products/expressionist/proteomics/
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.	http://www.dnastar.com/t-dnastar-lasergene.aspx http://www.genostar.com/category/products/gna/
iPathwayGuide	miRNA Activity, Molecule interactions DNA proteins interactions	Topology-based Analysis Advanced Correction Factors Prediction, Downstream Impact Analysis Meta Analysis	Advaita Bioinformatics: www.advaitabio.com
iBioguide	Genes, microRNAs, pathways, biological processes, molecular functions, cellular components, drugs, diseases,	find related genes, pathways, biological processes, molecular functions, cellular components, drugs, diseases,	https://ibioguide.advaitabio.com/
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	www.advaitabio.com 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	http://rgd.mcw.edu
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