Mercurial > repos > sblanck > smagexp
changeset 37:25b828010ca9 draft
planemo upload for repository https://github.com/sblanck/smagexp/tree/master/smagexp_tools commit bfd179bd7fb4796e21183e0e4de2fcf78ca35b7d
| author | sblanck |
|---|---|
| date | Mon, 25 Jun 2018 04:11:22 -0400 |
| parents | 22e1325aaa88 |
| children | c08b824e40cc |
| files | ImportDataFromMatrix.R MetaRNAseq.xml Recount.xml |
| diffstat | 3 files changed, 9 insertions(+), 10 deletions(-) [+] |
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--- a/ImportDataFromMatrix.R Fri Jun 22 04:30:31 2018 -0400 +++ b/ImportDataFromMatrix.R Mon Jun 25 04:11:22 2018 -0400 @@ -66,13 +66,10 @@ colnames(conditions)=c("source_name_ch1","description") phenodata<-new("AnnotatedDataFrame",data=conditions) -head(data) -conditions - eset=ExpressionSet(assayData=data,phenoData=phenodata,annotation=annotation) if (normalization == "quantile") { - eset <- normalize.ExpressionSet.quantiles(eset, transfn="log2") + eset <- normalize.ExpressionSet.quantiles(eset, transfn="log") } else if (normalization == "log2") { exprs(eset) = log2(exprs(eset)) }
--- a/MetaRNAseq.xml Fri Jun 22 04:30:31 2018 -0400 +++ b/MetaRNAseq.xml Mon Jun 25 04:11:22 2018 -0400 @@ -70,10 +70,12 @@ Given several DESeq2 results this tool runs a meta-analysis using the metaRNAseq R package. **Inputs** -At list 2 studies -- Results of DESeq2 study -- Number of replicate of the study +- At least 2 studies, and for each study + - Results of DESeq2 study + - Number of replicates of the study +- A FDR Threshold for a gene to be declared differentially expressed + **Results** - Venn Diagram or upsetR diagram (when the number of studies is greater than 2) summarizing the results of the meta-analysis @@ -84,8 +86,8 @@ - Loss : Number of genes that are identified differentially expressed in single studies but not in meta-analysis - DR (Integration-driven Discovery Rate) : corresponding proportion of IDD - IRR (Integration-driven Revision) : corresponding proportion of Loss - -- Fully sortable and requestable table, with gene annotations and hypertext links to NCBI gene database. + +It also generates a text file containing summarization of the results of each single analysis and meta-analysis. Potential conflicts between single analyses are indicated by zero values in the "signFC" column. ]]> </help>