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List of RNA-Seq bioinformatics tools (IV)  

2014-02-25 21:14:38|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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Visualization tools[edit]

  • Integrated Genome Browser IGB.
  • Integrative Genomics Viewer (IGV) IGV.

Functional, Network & Pathway Analysis Tools[edit]

  • GAGE is applicable independent of sample sizes, experimental design, assay platforms, and other types of heterogeneity (paper). This Biocondutor package also provides functions and data for pathway, GO and gene set analysis in general. Tutorials describe bothRNA-Seq pathway analysis workflows and microarray analysis workflows. The RNA-Seq workflows cover from preparation, reads counting, data preprocessing, gene set test, to pathway visualization in about 40 lines of codes.
  • Ingenuity Systems (commercial) iReport & IPA: Ingenuity’s IPA and iReport applications enable you to upload, analyze, and visualize RNA-Seq datasets, eliminating the obstacles between data and biological insight. Both IPA and iReport support identification, analysis and interpretation of differentially expressed isoforms between condition and control samples, and support interpretation and assessment of expression changes in the context of biological processes, disease and cellular phenotypes, and molecular interactions. Ingenuity iReport supports the upload of native Cuffdiff file format as well as gene expression lists. IPA supports the upload of gene expression lists.
  • Gene Set Association Analysis for RNA-Seq (GSAASeq): GSAASeq are computational methods that assess the differential expression of a pathway/gene set between two biological states based on sequence count data.

Further annotation tools for RNA-Seq data[edit]

  • seq2HLA seq2HLA is an annotation tool for obtaining an individual's HLA class I and II type and expression using standard NGS RNA-Seq data in fastq format. It comprises mapping RNA-Seq reads against a reference database of HLA alleles using bowtie, determining and reporting HLA type, confidence score and locus-specific expression level. This tool is developed in Python and R. It is available as console tool or Galaxy module. See also seqanswers/seq2HLA.
  • HLAminer HLAminer is a computational method for identifying HLA alleles directly from whole genome, exome and transcriptome shotgun sequence datasets. HLA allele predictions are derived by targeted assembly of shotgun sequence data and comparison to a database of reference allele sequences. This tool is developed in perl and it is available as console tool.
  • pasa pasa.

RNA-Seq Databases[edit]

Webinars and Presentations[edit]

References[edit]

  1. Jump up^ Wang Z, Gerstein M, Snyder M. (January 2009). "RNA-Seq: a revolutionary tool for transcriptomics". Nature Reviews Genetics 10 (1): 57–63.doi:10.1038/nrg2484. PMC 2949280. PMID 19015660.
  2. ^ Jump up to:a b Yang Liao, Gordon K Smyth and Wei Shi (2013). "The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote". Nucleic Acids Research 41. doi:10.1093/nar/gkt214. PMID 23558742.
  3. Jump up^ http://bioinformatics.oxfordjournals.org/content/29/1/15.full
  4. Jump up^ Cole Trapnell, Lior Pachter and Steven Salzberg (2009). "TopHat: discovering splice junctions with RNA-Seq". Bioinformatics 25 (9): 1105–1111.doi:10.1093/bioinformatics/btp120. PMC 2672628. PMID 19289445.
  5. Jump up^ Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold and Lior Pachter (2010). "Transcript assembly and abundance estimation from RNA-Seq reveals thousands of new transcripts and switching among isoforms". Nature Biotechnology 28 (5): 511–515. doi:10.1038/nbt.1621. PMC 3146043. PMID 20436464.
  6. Jump up^ Klambauer, G.; Unterthiner, T.; Hochreiter, S. (2013). "DEXUS: Identifying differential expression in RNA-Seq studies with unknown conditions".Nucleic Acids Research. doi:10.1093/nar/gkt834. PMID 24049071. edit
  7. Jump up^ Zerbino DR, Birney E (2008). "Velvet: Algorithms for de novo short read assembly using de Bruijn graphs". Genome Research 18 (5): 821–829.doi:10.1101/gr.074492.107. PMC 2336801. PMID 18349386.
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