cufflinks
Tophat
samtools
RNA-seq with Trinity
Physiological and transcriptomic responses to fishmeal-based diet and rapeseed meal-based diet in two strains of gibel carp (Carassius gibelio)
Transcriptomic response to soybean meal-based diets as the frst formulated feed in juvenile yellow perch (Perca favescens)
De novo characterization of the liver transcriptome of javelin goby Synechogobius hasta and analysis of its transcriptomic profile following waterborne copper exposure© wikimedia
Transcriptomic analysis of juvenile Chinese sea bass (Lateolabrax maculatus) anesthetized by MS-222 (tricaine methanesulfonate) and eugenol© wikimedia
Edger

Edger

Codes for hot to running EdgeR to call differential Expression Genes from RSEM result. (More details you can find in Trinity wiki)
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