메뉴 건너뛰기




Volumn 31, Issue 9, 2015, Pages 1496-1498

RNA-Rocket: An RNA-Seq analysis resource for infectious disease research

(19)  Warren, Andrew S a   Aurrecoechea, Cristina b   Brunk, Brian c,d   Desai, Prerak h   Emrich, Scott f,g   Giraldo Calderón, Gloria I f   Harb, Omar c,d   Hix, Deborah a   Lawson, Daniel e   Machi, Dustin a   Mao, Chunhong a   McClelland, Michael h   Nordberg, Eric a   Shukla, Maulik a   Vosshall, Leslie B i   Wattam, Alice R a   Will, Rebecca a   Yoo, Hyun Seung a   Sobral, Bruno a  


Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; BACTERIUM; COMPUTER PROGRAM; DISEASE CARRIER; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; HIGH THROUGHPUT SCREENING; PARASITE; PROCEDURES; SEQUENCE ANALYSIS;

EID: 84937798040     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv002     Document Type: Article
Times cited : (10)

References (20)
  • 1
    • 79951694175 scopus 로고    scopus 로고
    • Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
    • Aird, D. et al. (2011) Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol., 12. doi: 10.1186/gb-2011-12-2-r18.
    • (2011) Genome Biol., 12.
    • Aird, D.1
  • 2
    • 84876557849 scopus 로고    scopus 로고
    • EuPathDB: The eukaryotic pathogen database
    • Aurrecoechea, C. et al. (2013) EuPathDB: the eukaryotic pathogen database. Nucleic Acids Res., 41, D684-D691.
    • (2013) Nucleic Acids Res. , vol.41 , pp. D684-D691
    • Aurrecoechea, C.1
  • 3
    • 84861548193 scopus 로고    scopus 로고
    • Summarizing and correcting the GC content bias in high-throughput sequencing
    • Benjamini, Y. and Speed, T.P. (2012) Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Research, 40, e72.
    • (2012) Nucleic Acids Research , vol.40 , pp. e72
    • Benjamini, Y.1    Speed, T.P.2
  • 4
    • 79960905787 scopus 로고    scopus 로고
    • Galaxy: Aweb-based genome analysis tool for experimentalists
    • John Wiley & Sons, Inc, Hoboken, New Jersey
    • Blankenberg, D. et al. (2001) Galaxy: AWeb-Based Genome Analysis Tool for Experimentalists. Current Protocols in Molecular Biology. John Wiley & Sons, Inc, Hoboken, New Jersey.
    • (2001) Current Protocols in Molecular Biology
    • Blankenberg, D.1
  • 5
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: A flexible trimmer for Illumina sequence data
    • Bolger, A.M. et al. (2014) Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30, 2114-2120.
    • (2014) Bioinformatics , vol.30 , pp. 2114-2120
    • Bolger, A.M.1
  • 6
    • 25844449770 scopus 로고    scopus 로고
    • Galaxy: A platform for interactive large-scale genome analysis
    • Giardine, B. et al. (2005) Galaxy: A platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455.
    • (2005) Genome Res. , vol.15 , pp. 1451-1455
    • Giardine, B.1
  • 7
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks, J. et al. (2010) Galaxy: A comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11. doi: 10.1186/gb-2010-11-8-r86.
    • (2010) Genome Biol. , vol.11
    • Goecks, J.1
  • 8
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim, D. et al. (2013) TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol., 14, R36.
    • (2013) Genome Biol. , vol.14 , pp. R36
    • Kim, D.1
  • 9
    • 84875608234 scopus 로고    scopus 로고
    • The UCSC genome browser and associated tools
    • Kuhn, R.M. et al. (2013) The UCSC genome browser and associated tools. Briefings Bioinf., 14, 144-161.
    • (2013) Briefings Bioinf. , vol.14 , pp. 144-161
    • Kuhn, R.M.1
  • 10
    • 84859210032 scopus 로고    scopus 로고
    • Fast gapped-read alignment with Bowtie 2
    • Langmead, B. and Salzberg, S.L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
    • (2012) Nat. Methods , vol.9 , pp. 357-359
    • Langmead, B.1    Salzberg, S.L.2
  • 11
    • 78650568308 scopus 로고    scopus 로고
    • SAMStat: Monitoring biases in next generation sequencing data
    • Lassmann, T. et al. (2011) SAMStat: monitoring biases in next generation sequencing data. Bioinformatics, 27, 130-131.
    • (2011) Bioinformatics , vol.27 , pp. 130-131
    • Lassmann, T.1
  • 12
    • 78651317925 scopus 로고    scopus 로고
    • The european nucleotide archive
    • Leinonen, R. et al. (2011) The European Nucleotide Archive. Nucleic Acids Res., 39, D28-D31.
    • (2011) Nucleic Acids Res. , vol.39 , pp. D28-D31
    • Leinonen, R.1
  • 13
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li, H. et al. (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res., 18, 1851-1858.
    • (2008) Genome Res. , vol.18 , pp. 1851-1858
    • Li, H.1
  • 14
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li, H. et al. (2009) The sequence alignment/map format and SAMtools. Bioinformatics, 25, 2078-2079.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1
  • 15
    • 84858286227 scopus 로고    scopus 로고
    • VectorBase: Improvements to a bioinformatics resource for invertebrate vector genomics
    • Megy, K. et al. (2012) VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics. Nucleic Acids Res., 40, D729-D734.
    • (2012) Nucleic Acids Res. , vol.40 , pp. D729-D734
    • Megy, K.1
  • 16
    • 77951770756 scopus 로고    scopus 로고
    • BEDTools: A flexible suite of utilities for comparing genomic features
    • Quinlan, A.R. and Hall, I.M. (2010) BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics, 26, 841-842.
    • (2010) Bioinformatics , vol.26 , pp. 841-842
    • Quinlan, A.R.1    Hall, I.M.2
  • 17
    • 84859885816 scopus 로고    scopus 로고
    • Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
    • Trapnell, C. et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc., 7, 562-578.
    • (2012) Nat. Protoc. , vol.7 , pp. 562-578
    • Trapnell, C.1
  • 18
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: A revolutionary tool for transcriptomics
    • Wang, Z. et al. (2009) RNA-Seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet., 10, 57-63.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 57-63
    • Wang, Z.1
  • 19
    • 84891776599 scopus 로고    scopus 로고
    • PATRIC, the bacterial bioinformatics database and analysis resource
    • Wattam, A.R. et al. (2013) PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res., 42, D581-D591. doi: 10.1093/nar/gkt1099.
    • (2013) Nucleic Acids Res. , vol.42 , pp. D581-D591
    • Wattam, A.R.1
  • 20
    • 53849146020 scopus 로고    scopus 로고
    • Model-based analysis of ChIP-Seq (MACS)
    • Zhang, Y. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.
    • (2008) Genome Biol. , vol.9 , pp. R137
    • Zhang, Y.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.