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Volumn 261, Issue , 2017, Pages 149-156

KNIME for reproducible cross-domain analysis of life science data

Author keywords

KNIME; Life science; Workflow systems

Indexed keywords

DATA FLOW ANALYSIS; DATA VISUALIZATION; IMAGE PROCESSING; MASS SPECTROMETRY; OPEN SOURCE SOFTWARE; OPEN SYSTEMS;

EID: 85028043725     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2017.07.028     Document Type: Review
Times cited : (150)

References (46)
  • 2
    • 5344244656 scopus 로고    scopus 로고
    • R: A Language and Environment for Statistical Computing
    • R Foundation for Statistical Computing Vienna, Austria
    • R Development Core Team, R: A Language and Environment for Statistical Computing. 2008, R Foundation for Statistical Computing, Vienna, Austria ISBN:3-900051-07-0.
    • (2008)
    • R Development Core Team1
  • 3
    • 0003895851 scopus 로고    scopus 로고
    • Modern Applied Statistics with S
    • 4th ed. Springer New York
    • Venables, W.N., Ripley, B.D., Modern Applied Statistics with S. 4th ed., 2002, Springer, New York ISBN:0-387-95457-0.
    • (2002)
    • Venables, W.N.1    Ripley, B.D.2
  • 5
    • 77749296886 scopus 로고    scopus 로고
    • ggplot2: Elegant Graphics for Data Analysis
    • Springer-Verlag New York
    • Wickham, H., ggplot2: Elegant Graphics for Data Analysis. 2009, Springer-Verlag, New York.
    • (2009)
    • Wickham, H.1
  • 7
    • 23744500479 scopus 로고    scopus 로고
    • SciPy: Open Source Scientific Tools for Python
    • http://www.scipy.org/http://www.scipy.org/ (accessed 09.11.16)
    • Jones, E., Oliphant, T., Peterson, P., et al. SciPy: Open Source Scientific Tools for Python. 2001 http://www.scipy.org/http://www.scipy.org/ (accessed 09.11.16) http://www.scipy.org/.
    • (2001)
    • Jones, E.1    Oliphant, T.2    Peterson, P.3
  • 10
    • 84930630277 scopus 로고    scopus 로고
    • Deep learning
    • LeCun, Y., Bengio, Y., Hinton, G., Deep learning. Nature 521:7553 (2015), 436–444.
    • (2015) Nature , vol.521 , Issue.7553 , pp. 436-444
    • LeCun, Y.1    Bengio, Y.2    Hinton, G.3
  • 11
    • 85030097728 scopus 로고    scopus 로고
    • RDKit: Open-source cheminformatics, (accessed 11.04.13).
    • RDKit: Open-source cheminformatics, http://www.rdkit.org (accessed 11.04.13).
  • 14
    • 0033434080 scopus 로고    scopus 로고
    • Probability-based protein identification by searching sequence databases using mass spectrometry data
    • Perkins, D.N., Pappin, D.J., Creasy, D.M., Cottrell, J.S., Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20:18 (1999), 3551–3567, 10.1002/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2 http://www.ncbi.nlm.nih.gov/pubmed/10612281.
    • (1999) Electrophoresis , vol.20 , Issue.18 , pp. 3551-3567
    • Perkins, D.N.1    Pappin, D.J.2    Creasy, D.M.3    Cottrell, J.S.4
  • 15
    • 3142702204 scopus 로고    scopus 로고
    • TANDEM: matching proteins with tandem mass spectra
    • Craig, R., Beavis, R.C., TANDEM: matching proteins with tandem mass spectra. Bioinformatics (Oxford, England) 20:9 (2004), 1466–1467, 10.1093/bioinformatics/bth092 http://www.ncbi.nlm.nih.gov/pubmed/14976030.
    • (2004) Bioinformatics (Oxford, England) , vol.20 , Issue.9 , pp. 1466-1467
    • Craig, R.1    Beavis, R.C.2
  • 16
    • 50149117169 scopus 로고    scopus 로고
    • Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases
    • Kim, S., Gupta, N., Pevzner, P.A., Spectral probabilities and generating functions of tandem mass spectra: a strike against decoy databases. J. Proteome Res. 7:8 (2008), 3354–3363, 10.1021/pr8001244 http://www.pubmedcentral.nih.gov/articlerender.fcgi?.artid=2689316&tool=pmcentrez&rendertype=abstract.
    • (2008) J. Proteome Res. , vol.7 , Issue.8 , pp. 3354-3363
    • Kim, S.1    Gupta, N.2    Pevzner, P.A.3
  • 17
    • 84863609997 scopus 로고    scopus 로고
    • Toppas: a graphical workflow editor for the analysis of high-throughput proteomics data
    • Junker, J., Bielow, C., Bertsch, A., Sturm, M., Reinert, K., Kohlbacher, O., Toppas: a graphical workflow editor for the analysis of high-throughput proteomics data. J. Proteome Res. 11:7 (2012), 3914–3920.
    • (2012) J. Proteome Res. , vol.11 , Issue.7 , pp. 3914-3920
    • Junker, J.1    Bielow, C.2    Bertsch, A.3    Sturm, M.4    Reinert, K.5    Kohlbacher, O.6
  • 20
    • 84957922055 scopus 로고    scopus 로고
    • Peptide-level robust ridge regression improves estimation, sensitivity, and specificity in data-dependent quantitative label-free shotgun proteomics
    • Goeminne, L.J.E., Gevaert, K., Clement, L., Peptide-level robust ridge regression improves estimation, sensitivity, and specificity in data-dependent quantitative label-free shotgun proteomics. Molec. Cell. Proteomics: MCP 15:2 (2016), 657–668, 10.1074/mcp.M115.055897 http://www.ncbi.nlm.nih.gov/pubmed/26566788.
    • (2016) Molec. Cell. Proteomics: MCP , vol.15 , Issue.2 , pp. 657-668
    • Goeminne, L.J.E.1    Gevaert, K.2    Clement, L.3
  • 21
    • 84907033616 scopus 로고    scopus 로고
    • MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
    • Choi, M., Chang, C.-Y., Clough, T., Broudy, D., Killeen, T., MacLean, B., Vitek, O., MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics 30:17 (2014), 2524–2526, 10.1093/bioinformatics/btu305 http://www.ncbi.nlm.nih.gov/pubmed/24794931.
    • (2014) Bioinformatics , vol.30 , Issue.17 , pp. 2524-2526
    • Choi, M.1    Chang, C.-Y.2    Clough, T.3    Broudy, D.4    Killeen, T.5    MacLean, B.6    Vitek, O.7
  • 23
    • 39549090389 scopus 로고    scopus 로고
    • SeqAn an efficient, generic C++ library for sequence analysis
    • Döring, A., Weese, D., Rausch, T., Reinert, K., SeqAn an efficient, generic C++ library for sequence analysis. BMC Bioinformatics, 9(1), 2008, 11, 10.1186/1471-2105-9-11 http://www.ncbi.nlm.nih.gov/pubmed/18184432.
    • (2008) BMC Bioinformatics , vol.9 , Issue.1 , pp. 11
    • Döring, A.1    Weese, D.2    Rausch, T.3    Reinert, K.4
  • 24
    • 85030129092 scopus 로고    scopus 로고
    • SLIMM: Species Level Identification of Microorganisms from Metagenomes
    • Dadi, T.H., Renard, B.Y., Wieler, L.H., Semmler, T., Reinert, K., SLIMM: Species Level Identification of Microorganisms from Metagenomes. 2016.
    • (2016)
    • Dadi, T.H.1    Renard, B.Y.2    Wieler, L.H.3    Semmler, T.4    Reinert, K.5
  • 25
  • 27
    • 84976347324 scopus 로고    scopus 로고
    • KNIME for open-source bioimage analysis: a tutorial
    • Springer
    • Dietz, C., Berthold, M.R., KNIME for open-source bioimage analysis: a tutorial. Focus on Bio-Image Informatics, 2016, Springer, 179–197.
    • (2016) Focus on Bio-Image Informatics , pp. 179-197
    • Dietz, C.1    Berthold, M.R.2
  • 38
  • 39
    • 84902295958 scopus 로고    scopus 로고
    • Integrated and correlative high-throughput and super-resolution microscopy
    • Gunkel, M., Flottmann, B., Heilemann, M., Reymann, J., Erfle, H., Integrated and correlative high-throughput and super-resolution microscopy. Histochem. Cell Biol. 141:6 (2014), 597–603, 10.1007/s00418-014-1209-y.
    • (2014) Histochem. Cell Biol. , vol.141 , Issue.6 , pp. 597-603
    • Gunkel, M.1    Flottmann, B.2    Heilemann, M.3    Reymann, J.4    Erfle, H.5
  • 40
    • 77955364437 scopus 로고    scopus 로고
    • The KNIME Text Processing Plugin
    • Thiel, K., The KNIME Text Processing Plugin. 2009.
    • (2009)
    • Thiel, K.1
  • 41
    • 84922586090 scopus 로고    scopus 로고
    • Creating Usable Customer Intelligence from Social Media Data: Network Analytics Meets Text Mining
    • Thiel, K., Kötter, T., Berthold, D.M., Silipo, D.R., Winters, P., Creating Usable Customer Intelligence from Social Media Data: Network Analytics Meets Text Mining. 2009.
    • (2009)
    • Thiel, K.1    Kötter, T.2    Berthold, D.M.3    Silipo, D.R.4    Winters, P.5
  • 43
    • 84865126690 scopus 로고    scopus 로고
    • Scientific workflow systems: pipeline pilot and knime
    • Warr, W.A., Scientific workflow systems: pipeline pilot and knime. J. Comput.-Aid. Molec. Des. 26:7 (2012), 801–804.
    • (2012) J. Comput.-Aid. Molec. Des. , vol.26 , Issue.7 , pp. 801-804
    • Warr, W.A.1
  • 44
    • 77955801615 scopus 로고    scopus 로고
    • Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
    • Goecks, J., Nekrutenko, A., Taylor, J., Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11(8), 2010, R86.
    • (2010) Genome Biol. , vol.11 , Issue.8 , pp. R86
    • Goecks, J.1    Nekrutenko, A.2    Taylor, J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.