Ge SX, Son EW, Yao R (2018) iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. We also discuss the importance of critical interpretion of results (avoid p-hacking and rationalizing) and validation of significant pathways by using different methods and independent annotation databases.īioconductor DESeq2 Differential gene expression Gene set enrichment analysis Integrated differential expression and pathway analysis Pathway analysis RNA-seq Transcriptomic analysis iDEP. Using a public dataset on the effect of heat shock on mouse with and without functional Hsf1, we demonstrate how users can prepare data files and conduct in-depth analysis. Due to its intuitive user interface and massive annotation database, iDEP is being widely adopted for interactive analysis of RNA-seq data.
With iDEP, users can easily conduct exploratory data analysis, identify differentially expressed genes, and perform pathway analysis. We developed a user-friendly web app called iDEP (integrated differential expression and pathway analysis) to help biologists interpret read counts or other types of expression matrices derived from read mapping. The form and manner of this distribution makes it eligible for export under the License Exception ENC Technology Software Unrestricted (TSU) exception (see the BIS Export Administration Regulations, Section 740.13) for both object code and source code.RNA sequencing (RNA-seq) has become a routine method for transcriptomic profiling. Government Department of Commerce, Bureau of Industry and Security (BIS), has classified this software as Export Commodity Control Number (ECCN) 5D002.C.1, which includes information security software using or performing cryptographic functions with asymmetric algorithms. The country in which you currently reside may have restrictions on the import, possession, use, and/or re-export to another country, of encryption software.īEFORE using any encryption software, please check your country's laws, regulations and policies concerning the import, possession, or use, and re-export of encryption software, to see if this is permitted. This distribution includes cryptographic software.
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