| SMAGEXP (Statistical Meta Analalysis for Gene EXPression) integrates metaMA and metaRNAseq packages into Galaxy. We aim to propose a unified way to carry out meta-analysis of gene expression data, while taking care of their specificities. We have developed this tool suite to analyse microarray data from Gene Expression Omnibus (GEO) database or custom data from affymetrix microarrays. These data are then combined to carry out meta-analysis using metaMA package. SMAGEXP also offers to combine raw read counts from Next Generation Sequencing (NGS) experiments using DESeq2 and metaRNASeq package. In both cases, key values, independent from the technology type, are reported to judge the quality of the meta-analysis. |
hg clone https://toolshed.g2.bx.psu.edu/repos/sblanck/smagexp
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| Performs gene expression analysis thanks to limma | 1.0.0 | 16.01 | |
| Quality control and normalization of a custom matrix expression data | 1.0.0 | 16.01 | |
| Quality control and normalization of affymetrix expression data | 1.0.1 | 16.01 | |
| Performs meta-analysis thanks to metaRNAseq | 1.1.0 | 16.01 | |
| Get rna-seq count data with R recount Package | 1.0.0 | 16.01 | |
| Performs meta-analysis thanks to metaMA. | 1.0.0 | 16.01 | |
| GEOQuery wrapper | 1.0.0 | 16.01 | |