TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data
High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy. Numerous bioconductor packages have been developed for the statistical analysis of RNA-Seq data. However, these tools focus on specifi...
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| Format: | Article |
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BioMed Central
2017-03-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-15-51.pdf |
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| author | Jae Hyun Lim Soo Youn Lee Ju Han Kim |
| author_facet | Jae Hyun Lim Soo Youn Lee Ju Han Kim |
| author_sort | Jae Hyun Lim |
| collection | DOAJ |
| description | High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy. Numerous bioconductor packages have been developed for the statistical analysis of RNA-Seq data. However, these tools focus on specific aspects of the data analysis pipeline, and are difficult to appropriately integrate with one another due to their disparate data structures and processing methods. They also lack visualization methods to confirm the integrity of the data and the process. In this paper, we propose an R-based RNA-Seq analysis pipeline called TRAPR, an integrated tool that facilitates the statistical analysis and visualization of RNA-Seq expression data. TRAPR provides various functions for data management, the filtering of low-quality data, normalization, transformation, statistical analysis, data visualization, and result visualization that allow researchers to build customized analysis pipelines. |
| format | Article |
| id | doaj-art-4ad73091141442d4a4e81973f4ef5057 |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2017-03-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-4ad73091141442d4a4e81973f4ef50572025-02-02T15:16:26ZengBioMed CentralGenomics & Informatics1598-866X2234-07422017-03-01151515310.5808/GI.2017.15.1.51206TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq DataJae Hyun Lim0Soo Youn Lee1Ju Han Kim2Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics and Systems Biomedical Informatics Research Center, Seoul National University College of Medicine, Seoul 110799, Korea.Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics and Systems Biomedical Informatics Research Center, Seoul National University College of Medicine, Seoul 110799, Korea.Seoul National University Biomedical Informatics (SNUBI), Division of Biomedical Informatics and Systems Biomedical Informatics Research Center, Seoul National University College of Medicine, Seoul 110799, Korea.High-throughput transcriptome sequencing, also known as RNA sequencing (RNA-Seq), is a standard technology for measuring gene expression with unprecedented accuracy. Numerous bioconductor packages have been developed for the statistical analysis of RNA-Seq data. However, these tools focus on specific aspects of the data analysis pipeline, and are difficult to appropriately integrate with one another due to their disparate data structures and processing methods. They also lack visualization methods to confirm the integrity of the data and the process. In this paper, we propose an R-based RNA-Seq analysis pipeline called TRAPR, an integrated tool that facilitates the statistical analysis and visualization of RNA-Seq expression data. TRAPR provides various functions for data management, the filtering of low-quality data, normalization, transformation, statistical analysis, data visualization, and result visualization that allow researchers to build customized analysis pipelines.http://genominfo.org/upload/pdf/gni-15-51.pdfbase sequencegene expression profilingmolecular sequence dataprogramming languagessequence analysis/RNAsoftware |
| spellingShingle | Jae Hyun Lim Soo Youn Lee Ju Han Kim TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data Genomics & Informatics base sequence gene expression profiling molecular sequence data programming languages sequence analysis/RNA software |
| title | TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data |
| title_full | TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data |
| title_fullStr | TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data |
| title_full_unstemmed | TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data |
| title_short | TRAPR: R Package for Statistical Analysis and Visualization of RNA-Seq Data |
| title_sort | trapr r package for statistical analysis and visualization of rna seq data |
| topic | base sequence gene expression profiling molecular sequence data programming languages sequence analysis/RNA software |
| url | http://genominfo.org/upload/pdf/gni-15-51.pdf |
| work_keys_str_mv | AT jaehyunlim traprrpackageforstatisticalanalysisandvisualizationofrnaseqdata AT sooyounlee traprrpackageforstatisticalanalysisandvisualizationofrnaseqdata AT juhankim traprrpackageforstatisticalanalysisandvisualizationofrnaseqdata |