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|Alternative name||flow difference metric|
|Software type||Application/Script, Package/Module|
|Interface||Command line interface|
|Restrictions to use||None|
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Publication for flow difference metric
A survey of best practices for RNA seq data analysis
[…] r differences. By integrating the two steps, the uncertainty in the first step is taken into consideration when performing the statistical analysis to look for differential isoform expression . The flow difference metric (FDM) uses aligned cumulative transcript graphs from mapped exon reads and junction reads to infer isoforms and the Jensen-Shannon divergence to measure the difference . Recen […]
Comparisons of computational methods for differential alternative splicing detection using RNA seq in plant systems
[…] of programs is not exhaustive; however, we have selected a set of programs which represent a variety of approaches. Due to our limited human resources and computational power, the current versions of FDM  and JuncBase  met our criteria but were excluded from this study. FDM uses a splice graph representation of aligned RNA-seq data and Jensen Shannon Divergence (JSD) to measure the difference […]
Efficient experimental design and analysis strategies for the detection of differential expression using RNA Sequencing
[…] ecifically to appropriately handle expected technical and biological variation arising from RNA-Seq experiments. A non-exhaustive list of these algorithms is: edgeR , DESeq , NBPSeq , BBSeq , FDM , RSEM , NOISeq , Myrna , Cuffdiff . A thorough comparison of these packages’ performance with datasets of different properties falls beyond the scope of this study, however before consi […]
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