Software
BCMC (Biomarker Categorization in Meta-analysis by Concordance)
- R package to perform meta-analysis of multiple transcriptomic studies for biomarker detection and categorization by simultaneously considering the biological and statistical significance as well as the concordant pattern across studies. [package]
CoxTOTEM (TwO-sTage variable sElection procedure for Multiple studies)
- R package to detect survival associated biomarkers with multiple genomic studies. [package]
CAMO (Congruence Analysis of Model Organisms)
- R package and Shiny application to perform congruence analysis and functional charaterization for comparison of differential transcriptomic systems across model organisms, including numerous downstream bioinformatic tools for text mining, pathway clustering and topology. [package] [manual] [Shiny application]
MetaOmics
- R Shiny application to perform comprehensive transcriptomic meta-analysis for seven different biological purposes. [package] [tutorial]
MetaDE (part of MetaOmics)
BayesMetaSeq
- R package to combine multiple RNA-seq studies by Bayesian hierarchical model for detecting differentially expressed genes and biomarker categorization. [package] [manual]
CBM (Cross-platform Bayesian Meta-analysis)
- R package to combine multiple RNA-seq and microarray studies by Bayesian hierarchical model for detecting differentially expressed genes. [package] [manual]