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| DESeq | edgeR | DEXSeq | Cuffdiff | |
|---|---|---|---|---|
| Normalization | Median scaling size factor | Median scaling size factor /TMM | Median scaling size factor | FPKM (a slight variation on RPKM) |
| Distribution | Negative binomial | Negative binomial | Negative binomial | Negative binomial |
| DE Test | Negative binomial test | Fisher exact test | Modified T test | T test |
| Advantages | Straightforward, fast, has a method to work on data with no replicates
| Straightforward, fast, good with small number of replicates. Can handle comparisons across multiple conditions | Good for identifying exon-usage changes | Good for identifying isoform-level changes, splicing changes, promotor changes. Not as straightforward, somewhat of a black box |
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