In shiauck/cummeRbund_on_RSQLite2.0: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
Run Report
Run Parameters
alpha=0.05
runInfo()
Global Statistics
cuff
FPKM distributions
csDensity(genes(cuff))
csDensity(isoforms(cuff))
Scatterplots
csScatterMatrix(genes(cuff),logMode=T)
Replicate Information
Model fit
Differential Expression Analysis
Significant Genes
sigMatrix(cuff,level="genes")
csVolcanoMatrix(genes(cuff),alpha=alpha)
sigGeneIDs<-getSig(cuff,alpha=alpha)
sigGenes<-getGenes(cuff,sigGeneIDs)
There are r length(sigGeneIDs) significantly different genes at a r alpha*100$\%$ FDR.
Visualizations
csHeatmap(sigGenes,cluster="both",labRow=F)
Significant Isoforms
sigMatrix(cuff,level="isoforms")
shiauck/cummeRbund_on_RSQLite2.0 documentation built on May 5, 2019, 12:33 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Run Report
Run Parameters
alpha=0.05 runInfo()
Global Statistics
cuff
FPKM distributions
csDensity(genes(cuff)) csDensity(isoforms(cuff))
Scatterplots
csScatterMatrix(genes(cuff),logMode=T)
Replicate Information
Model fit
Differential Expression Analysis
Significant Genes
sigMatrix(cuff,level="genes")
csVolcanoMatrix(genes(cuff),alpha=alpha)
sigGeneIDs<-getSig(cuff,alpha=alpha) sigGenes<-getGenes(cuff,sigGeneIDs)
There are r length(sigGeneIDs) significantly different genes at a r alpha*100$\%$ FDR.
Visualizations
csHeatmap(sigGenes,cluster="both",labRow=F)
Significant Isoforms
sigMatrix(cuff,level="isoforms")
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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