Skip to main content

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 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