DEAR-O: Differential Expression Analysis based on RNA-seq data - Online
نویسندگان
چکیده
Summary: Differential expression analysis using high-throughput RNA sequencing (RNA-seq) data is widely applied in transcriptomic studies and many software tools have been developed for this purpose. Active development of existing popular tools, together with emergence of new tools means that studies comparing the performance of differential expression analysis methods become rapidly out-of-date. In order to enable researchers to evaluate new and updated software in a timely manner, we developed DEAR-O, a user-friendly platform for performance evaluation of differential expression analysis based on RNA-seq data. The platform currently includes four of the most popular tools: DESeq, DESeq2, edgeR and Cuffdiff2. Based on the DEAR-O platform, researchers can evaluate the performance of different tools, or the same tool with different versions, with a customised number of biological replicates using already curated RNA-seq datasets. We also initiated an online forum for discussion of RNA-seq differential expression analysis. Through this forum, new useful tools and benchmarking datasets can be introduced. Our platform will be actively maintained to ensure new major versions of existing tools and new popular tools are included. DEAR-O will serve the community by providing timely evaluations of tools, versions and number of replicates for RNA-seq differential expression analysis. Availability and implementation: The DEAR-O platform is available at http://cnsgenomics.com/software/dear-o; the online discussion forum is https://groups.google.com/d/forum/dear-o Contact: [email protected] and [email protected]
منابع مشابه
Regulatory effects of cis- and trans-LncRNAs on differential expression of genes following infection with viral hemorrhagic septicemia virus in rainbow trout (Oncorhynchus mykiss)
In this study the cis and trans regulatory effect of long non-coding genes (lncRNA) on the expression of genes in fish infected by Viral hemorrhagic septicemia virus (VHS) was investigated using RNA-seq technology. At the end of experimental period (the thirty fifth day), total RNA was extracted from spleen tissue (group treated with virus) and physiological serum (control group) was used to pr...
متن کاملPolyester: simulating RNA-seq datasets with differential transcript expression
MOTIVATION Statistical methods development for differential expression analysis of RNA sequencing (RNA-seq) requires software tools to assess accuracy and error rate control. Since true differential expression status is often unknown in experimental datasets, artificially constructed datasets must be utilized, either by generating costly spike-in experiments or by simulating RNA-seq data. RES...
متن کاملInvestigating the Function of Predicted Proteins from RNA-Seq Data in Holstein and Cholistani Cattle Breeds
This study was performed to determine the digital expression profile of different genes expressed in Holstein and Cholistani breeds as well as to evaluate the performance of predicted proteins derived from differentially expressed genes between these two breeds using RNA-Seq data. For this purpose, the whole mRNA sequence for a blood sample of American Holstein and Pakistani Cholistani cattle p...
متن کاملRiborex: fast and flexible identification of differential translation from Ribo-seq data
Motivation Global analysis of translation regulation has recently been enabled by the development of Ribosome Profiling, or Ribo-seq, technology. This approach provides maps of ribosome activity for each expressed gene in a given biological sample. Measurements of translation efficiency are generated when Ribo-seq data is analyzed in combination with matched RNA-seq gene expression profiles. Ex...
متن کاملAccurate differential gene expression analysis for RNA-Seq data without replicates
Despite the fact that many RNA-Seq experiments do not use biological replicates, most of the existing differential gene expression analysis for RNA-Seq data are designed to work with replicates. We present a novel method for differential gene expression analysis based on bootstrapping. We also discuss the use of different normalization methods with Fisher’s exact test. We compare the methods we...
متن کامل