Here is a list of tools which can be used to process data for silencing RNA. Unsure how to proceed? Try our getting started guide.
baySeq is a package for calculating Differential Expression in Solexa-type, or count, data for the R Project For Statistical Computing. It was previously available on these pages but is now part of Bioconductor. For more information please see the Bioconductor website.
For details on the methods being used, consult Hardcastle et al. (2009) Empirical Bayesian methods for estimating differential expression in count data.
At-TAX is a whole genome tiling array resource for developmental expression analysis and transcript identification in Arabidopsis thaliana. Tiling array hybridization intensities, probe set definitions for Arabidopsis genes and segmentations into exonic and background regions are visualized in a genome browser. Visualizations of gene expression and cross-platform comparisons are available through tileViz.
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SHORE is a tool for the analysis of Illumina Genome Analyzer expression data, including both mRNA sequencing (mRNA-seq) and small RNA sequencing (sRNA-seq). It includes preprocessing and quality filtering of Illumina GA reads, mapping of reads against a reference genome, splice site detection for mRNA-seq as well as quantitative expression analysis and visualization.
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