RobiNA: A user-friendly, integrated software solution for RNA-Seq-based transcriptomics

Nucleic Acids Research

Volumn 40, Issue W1, 2012, Pages

  Lohse, Marc ^a   Bolger, Anthony M ^a   Nagel, Axel ^a   Fernie, Alisdair R ^a   Lunn, John E ^a   Stitt, Mark ^a   Usadel, Björn ^a,b,c  

^a MAX PLANCK INSTITUTE OF MOLECULAR PLANT PHYSIOLOGY   (Germany)

^b RWTH AACHEN UNIVERSITY   (Germany)

^c FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER INTERFACE; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENE MAPPING; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; PRIORITY JOURNAL; RNA SEQUENCE; SEQUENCE ALIGNMENT; TRANSCRIPTOMICS;

GENE EXPRESSION PROFILING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTERNET; SEQUENCE ANALYSIS, RNA; SOFTWARE; SYSTEMS INTEGRATION; USER-COMPUTER INTERFACE;

EID: 84864483625     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks540     Document Type: Article

References (27)

1. Wheeler, D.L., Barrett, T., Benson, D.A., Bryant, S.H., Canese, K., Chetvernin, V., Church, D.M., Dicuccio, M., Edgar, R., Federhen, S. et al. (2008) Database resources of the National Center for Biotechnology Information. Nucleic Acids Res, 36, D13-D21.
2. Leinonen, R., Akhtar, R., Birney, E., Bower, L., Cerdeno-Tarraga, A., Cheng, Y., Cleland, I., Faruque, N., Goodgame, N., Gibson, R. et al. (2010) The European Nucleotide Archive. Nucleic Acids Res, 39, D28-D31.
3. Bajgain, P., Richardson, B.A., Price, J.C., Cronn, R.C. and Udall, J.A. (2011) Transcriptome characterization and polymorphism detection between subspecies of big sagebrush (Artemisia tridentata). BMC Genomics, 12, 370.
4. Wang, T.Y., Chen, H.L., Lu, M.Y., Chen, Y.C., Sung, H.M., Mao, C.T., Cho, H.Y., Ke, H.M., Hwa, T.Y., Ruan, S.K. et al. (2011) Functional characterization of cellulases identified from the cow rumen fungus neocallimastix patriciarum W5 by transcriptomic and secretomic analyses. Biotechnol. Biofuels, 4, 24.
5. Siebert, S., Robinson, M.D., Tintori, S.C., Goetz, F., Helm, R.R., Smith, S.A., Shaner, N., Haddock, S.H. and Dunn, C.W. (2011) Differential gene expression in the Siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows. PloS One, 6, e22953.
6. Su, C.L., Chao, Y.T., Alex Chang, Y.C., Chen, W.C., Chen, C.Y., Lee, A.Y., Hwa, K.T. and Shih, M.C. (2011) De novo assembly of expressed transcripts and global analysis of phalaenopsis aphrodite transcriptome. Plant Cell Physiol., 52, 1501-1514.
7. Li, H. and Homer, N. (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief Bioinform, 11, 473-483.
8. Oshlack, A., Robinson, M.D. and Young, M.D. (2010) From RNAseq reads to differential expression results. Genome Biol., 11, 220.
9. Gentleman, R.C., Carey, V.J., Bates, D.M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80.
10. Robinson, M.D., McCarthy, D.J. and Smyth, G.K. (2009) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140.
11. Anders, S. and Huber, W. (2010) Differential expression analysis for sequence count data. Genome Biol., 11, R106.
12. Hardcastle, T.J. and Kelly, K.A. (2010) Bayseq: empirical bayesian methods for identifying differential expression in sequence count data. BMC Bioinformatics, 11, 422.
13. Reich, M., Liefeld, T., Gould, J., Lerner, J., Tamayo, P. and Mesirov, J.P. (2006) GenePattern 2.0. Nat Genet, 38, 500-501.
14. Langmead, B., Hansen, K.D. and Leek, J.T. (2010) Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biol, 11, R83.
15. Goecks, J., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol, 11, R86.
16. Giardine, B., Riemer, C., Hardison, R.C., Burhans, R., Elnitski, L., Shah, P., Zhang, Y., Blankenberg, D., Albert, I., Taylor, J. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res, 15, 1451-1455.
17. Blankenberg, D., Von Kuster, G., Coraor, N., Ananda, G., Lazarus, R., Mangan, M., Nekrutenko, A. and Taylor, J. (2010) Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol, 89, 19.10.1-19.10.21.
18. Xu, G., Deng, N., Zhao, Z., Judeh, T., Flemington, E. and Zhu, D. (2011) SAMMate: a GUI tool for processing short read alignments in SAM/BAM format. Source Code Biol Med, 6, 2.
19. Langmead, B., Trapnell, C., Pop, M. and Salzberg, S.L. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol, 10, R25.
20. Frazee, A.C., Langmead, B. and Leek, J.T. (2011) ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. BMC Bioinformatics, 12, 449.
21. Hansen, K.D., Brenner, S.E. and Dudoit, S. (2010) Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res, 38, e131.
22. Bullard, J.H., Purdom, E., Hansen, K.D. and Dudoit, S. (2010) Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics, 18, 94.
23. Benjamini, Y. and Speed, T.P. (2012) Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res, 40, e72.
24. Risso, D., Schwartz, K., Sherlock, G. and Dudoit, S. (2011) GCcontent normalization for RNA-Seq data. BMC Bioinformatics, 12, 480.
25. Usadel, B., Poree, F., Nagel, A., Lohse, M., Czedik-Eysenberg, A. and Stitt, M. (2009) A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plant Cell Environ, 32, 1211-1229.
26. Lohse, M., Nunes-Nesi, A., Kruger, P., Nagel, A., Hannemann, J., Giorgi, F.M., Childs, L., Osorio, S., Walther, D., Selbig, J. et al. (2010) Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis. Plant Physiol, 153, 642-651.
27. Holland, R.C., Down, T.A., Pocock, M., Prlic, A., Huen, D., James, K., Foisy, S., Drager, A., Yates, A., Heuer, M. et al. (2008) BioJava: an open-source framework for bioinformatics. Bioinformatics, 24, 2096-2097.