-
1
-
-
0002339335
-
Graphs in statistical analysis
-
Anscombe, F. J., Graphs in statistical analysis. Am. Stat. 1973, 27, 17-21.
-
(1973)
Am. Stat.
, vol.27
, pp. 17-21
-
-
Anscombe, F.J.1
-
3
-
-
36749063069
-
-
Chapman & Hall/CRC Press, Boca Raton, FL, USA .
-
Murrell, P., R Graphics, Second Edition. Chapman & Hall/CRC Press, Boca Raton, FL, USA 2011.
-
(2011)
R Graphics, Second Edition
-
-
Murrell, P.1
-
5
-
-
28744458859
-
Bioconductor: open software development for computational biology and bioinformatics
-
Gentleman, R., Carey, V. J., Bates, D. M., Bolstad, B. et al., Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5, R80.
-
(2004)
Genome Biol.
, vol.5
, pp. R80
-
-
Gentleman, R.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
-
7
-
-
84890569154
-
Using R and Bioconductor for proteomics data analysis
-
Gatto, L., Christoforou, A., Using R and Bioconductor for proteomics data analysis. Biochim. Biophys. Acta 2014, 1844, 42-51.
-
(2014)
Biochim. Biophys. Acta
, vol.1844
, pp. 42-51
-
-
Gatto, L.1
Christoforou, A.2
-
8
-
-
79953289737
-
Mapping of signaling networks through synthetic genetic interaction analysis by RNAi
-
Horn, T., Sandmann, T., Fischer, B., Axelsson, E. et al., Mapping of signaling networks through synthetic genetic interaction analysis by RNAi. Nat. Methods 2011, 8, 341-346.
-
(2011)
Nat. Methods
, vol.8
, pp. 341-346
-
-
Horn, T.1
Sandmann, T.2
Fischer, B.3
Axelsson, E.4
-
9
-
-
84862798576
-
Isoelectric point optimization using peptide descriptors and support vector machines
-
Perez-Riverol, Y., Audain, E., Millan, A., Ramos, Y. et al., Isoelectric point optimization using peptide descriptors and support vector machines. J . Proteomics 2012, 75, 2269-2274.
-
(2012)
J . Proteomics
, vol.75
, pp. 2269-2274
-
-
Perez-Riverol, Y.1
Audain, E.2
Millan, A.3
Ramos, Y.4
-
10
-
-
59249094016
-
caret: Classification and Regression Training
-
R package version 6.0-41, 2015.
-
Kuhn, M., caret: Classification and Regression Training. R package version 6.0-41, 2015.
-
-
-
Kuhn, M.1
-
11
-
-
84904409942
-
Building and exploring an integrated human kinase network: global organization and medical entry points
-
Colinge, J., Csar-Razquin, A., Huber, K., Breitwieser, F. P. et al., Building and exploring an integrated human kinase network: global organization and medical entry points. J. Proteomics 2014, 107, 113-127.
-
(2014)
J. Proteomics
, vol.107
, pp. 113-127
-
-
Colinge, J.1
Csar-Razquin, A.2
Huber, K.3
Breitwieser, F.P.4
-
12
-
-
79952752375
-
System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation
-
Rigbolt, K. T., Prokhorova, T. A., Akimov, V., Henningsen, J. et al., System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. Sci. Signal 2011, 4, rs3.
-
(2011)
Sci. Signal
, vol.4
, pp. rs3
-
-
Rigbolt, K.T.1
Prokhorova, T.A.2
Akimov, V.3
Henningsen, J.4
-
13
-
-
84881112764
-
Quantitative proteomics reveals the temperature-dependent proteins encoded by a series of cluster genes in thermoanaerobacter tengcongensis
-
Chen, Z., Wen, B., Wang, Q., Tong, W. et al., Quantitative proteomics reveals the temperature-dependent proteins encoded by a series of cluster genes in thermoanaerobacter tengcongensis. Mol. Cell Proteomics 2013, 12, 2266-2277.
-
(2013)
Mol. Cell Proteomics
, vol.12
, pp. 2266-2277
-
-
Chen, Z.1
Wen, B.2
Wang, Q.3
Tong, W.4
-
14
-
-
79958198057
-
General statistical modeling of data from protein relative expression isobaric tags
-
Breitwieser, F. P., Müller, A., Dayon, L., Köcher, T. et al., General statistical modeling of data from protein relative expression isobaric tags. J. Proteome Res. 2011, 10, 2758-2766.
-
(2011)
J. Proteome Res.
, vol.10
, pp. 2758-2766
-
-
Breitwieser, F.P.1
Müller, A.2
Dayon, L.3
Köcher, T.4
-
15
-
-
12444345515
-
Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS
-
Thompson, A., Schäfer, J., Kuhn, K., Kienle, S. et al., Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal. Chem. 2003, 75, 1895-1904.
-
(2003)
Anal. Chem.
, vol.75
, pp. 1895-1904
-
-
Thompson, A.1
Schäfer, J.2
Kuhn, K.3
Kienle, S.4
-
16
-
-
84893841383
-
Identification of trans-golgi network proteins in arabidopsis thaliana root tissue
-
Groen, A. J., Sancho-Andrs, G., Breckels, L. M., Gatto, L. et al., Identification of trans-golgi network proteins in arabidopsis thaliana root tissue. J. Proteome Res. 2014, 13, 763-776.
-
(2014)
J. Proteome Res.
, vol.13
, pp. 763-776
-
-
Groen, A.J.1
Sancho-Andrs, G.2
Breckels, L.M.3
Gatto, L.4
-
17
-
-
84907789935
-
Label-free protein quantification for plant golgi protein localization and abundance
-
Nikolovski, N., Shliaha, P. V., Gatto, L., Dupree, P., Lilley, K. S., Label-free protein quantification for plant golgi protein localization and abundance. Plant Physiol. 2014, 166, 1033-1043.
-
(2014)
Plant Physiol.
, vol.166
, pp. 1033-1043
-
-
Nikolovski, N.1
Shliaha, P.V.2
Gatto, L.3
Dupree, P.4
Lilley, K.S.5
-
18
-
-
84899504030
-
Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata
-
Gatto, L., Breckels, L. M., Wieczorek, S., Burger, T., Lilley, K. S., Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata. Bioinformatics 2014, 30, 1322-1324.
-
(2014)
Bioinformatics
, vol.30
, pp. 1322-1324
-
-
Gatto, L.1
Breckels, L.M.2
Wieczorek, S.3
Burger, T.4
Lilley, K.S.5
-
22
-
-
84856104821
-
Msnbase-an r/bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation
-
Gatto, L., Lilley, K. S., Msnbase-an r/bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. Bioinformatics 2012, 28, 288-289.
-
(2012)
Bioinformatics
, vol.28
, pp. 288-289
-
-
Gatto, L.1
Lilley, K.S.2
-
23
-
-
1342288026
-
affy-analysis of Affymetrix GeneChip data at the probe level
-
Gautier, L., Cope, L., Bolstad, B. M., Irizarry, R. A., affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics 2004, 20, 307-315.
-
(2004)
Bioinformatics
, vol.20
, pp. 307-315
-
-
Gautier, L.1
Cope, L.2
Bolstad, B.M.3
Irizarry, R.A.4
-
24
-
-
84926507971
-
Limma powers differential expression analyses for RNA-sequencing and microarray studies
-
Ritchie, M. E., Phipson, B., Wu, D., Hu, Y. et al., Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015, 43.
-
(2015)
Nucleic Acids Res.
, vol.43
-
-
Ritchie, M.E.1
Phipson, B.2
Wu, D.3
Hu, Y.4
-
25
-
-
61749097406
-
marray: Exploratory analysis for two-color spotted microarray data
-
R package version 1.45.0, 2009.
-
Yang, Y. H., marray: Exploratory analysis for two-color spotted microarray data. R package version 1.45.0, 2009.
-
-
-
Yang, Y.H.1
-
26
-
-
84924629414
-
Moderated estimation of fold change and dispersion for rna-seq data with deseq2
-
Love, M. I., Huber, W., Anders, S., Moderated estimation of fold change and dispersion for rna-seq data with deseq2. Genome Biol. 2014, 15, 550.
-
(2014)
Genome Biol.
, vol.15
, pp. 550
-
-
Love, M.I.1
Huber, W.2
Anders, S.3
-
27
-
-
75249087100
-
Edger: a bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M. D., McCarthy, D. J., Smyth, G. K., Edger: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 2010, 26, 139-140.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
McCarthy, D.J.2
Smyth, G.K.3
-
28
-
-
84891796097
-
Proteomexchange provides globally coordinated proteomics data submission and dissemination
-
Vizcaíno, J. A.
-
Vizcaíno, J. A., Deutsch, E. W., Wang, R., Csordas, A. et al., Proteomexchange provides globally coordinated proteomics data submission and dissemination. Nat. Biotechnol. 2014, 32, 223-226.
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 223-226
-
-
Deutsch, E.W.1
Wang, R.2
Csordas, A.3
-
29
-
-
85081869892
-
-
RColorBrewer: ColorBrewer palettes. R package version 1.0-5
-
Neuwirth, E., RColorBrewer: ColorBrewer palettes. R package version 1.0-5, 2011.
-
(2011)
-
-
Neuwirth, E.1
-
30
-
-
19944432197
-
Multiplexed protein quantitation in saccharomyces cerevisiae using amine-reactive isobaric tagging reagents
-
Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B. et al., Multiplexed protein quantitation in saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol. Cell Proteomics 2004, 3, 1154-1169.
-
(2004)
Mol. Cell Proteomics
, vol.3
, pp. 1154-1169
-
-
Ross, P.L.1
Huang, Y.N.2
Marchese, J.N.3
Williamson, B.4
-
31
-
-
85081867963
-
-
shiny: Web Application Framework for R. R package version 0.10.1
-
RStudio Inc., shiny: Web Application Framework for R. R package version 0.10.1, 2014.
-
(2014)
-
-
-
32
-
-
85081867123
-
-
ggvis: Interactive grammar of graphics. R package version 0.4
-
RStudio Inc., ggvis: Interactive grammar of graphics. R package version 0.4, 2014.
-
(2014)
-
-
-
33
-
-
84918570544
-
-
O'Reilly Media, Sebastopol, CA, USA .
-
Chang, W., R Graphics Cookbook. O'Reilly Media, Sebastopol, CA, USA 2012.
-
(2012)
R Graphics Cookbook
-
-
Chang, W.1
-
34
-
-
85081861665
-
msmsTests: LC-MS/MS Differential Expression Tests
-
Gregori, J., Sanchez, A., Villanueva, J., msmsTests: LC-MS/MS Differential Expression Tests. R package version 1.5.0, 2013.
-
(2013)
R package version 1.5.0
-
-
Gregori, J.1
Sanchez, A.2
Villanueva, J.3
-
35
-
-
84907033616
-
MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments
-
Choi, M., Chang, C. Y., Clough, T., Broudy, D. et al., MSstats: an R package for statistical analysis of quantitative mass spectrometry-based proteomic experiments. Bioinformatics 2014, 30, 2524-2526.
-
(2014)
Bioinformatics
, vol.30
, pp. 2524-2526
-
-
Choi, M.1
Chang, C.Y.2
Clough, T.3
Broudy, D.4
-
36
-
-
85081865450
-
ProteinArrayAnalyzer (PAA): A Novel R/Bioconductor Package for Autoimmune Biomarker Discovery with Protein Microarrays
-
Turewicz, M., ProteinArrayAnalyzer (PAA): A Novel R/Bioconductor Package for Autoimmune Biomarker Discovery with Protein Microarrays. R package version 1.1.0, 2014.
-
(2014)
R package version 1.1.0
-
-
Turewicz, M.1
-
37
-
-
85081872916
-
msmsEDA: Exploratory Data Analysis of LC-MS/MS data by spectral counts
-
Gregori, J., Sanchez, A., Villanueva, J., msmsEDA: Exploratory Data Analysis of LC-MS/MS data by spectral counts. R package version 1.5.0, 2014.
-
(2014)
R package version 1.5.0
-
-
Gregori, J.1
Sanchez, A.2
Villanueva, J.3
-
38
-
-
84907251310
-
FactoMineR: Multivariate Exploratory Data Analysis and Data Mining with R
-
Husson, F., Josse, J., Le, S., Mazet, J., FactoMineR: Multivariate Exploratory Data Analysis and Data Mining with R. R package version 1.28, 2014.
-
(2014)
R package version 1.28
-
-
Husson, F.1
Josse, J.2
Le, S.3
Mazet, J.4
-
40
-
-
85081870080
-
Mfuzz: Soft clustering of time series gene expression data
-
Futschik, M., Mfuzz: Soft clustering of time series gene expression data. R package version 2.27.0, 2014.
-
(2014)
R package version 2.27.0
-
-
Futschik, M.1
-
41
-
-
85081868842
-
dendextend: Extending R's dendrogram functionality
-
Galili, T., dendextend: Extending R's dendrogram functionality. R package version 0.17.5, 2014.
-
(2014)
R package version 0.17.5
-
-
Galili, T.1
-
42
-
-
78650575601
-
gplots: Various R Programming Tools for Plotting Data
-
Warnes, G. R., Bolker, B., Bonebakker, L., Gentleman, R. et al., gplots: Various R Programming Tools for Plotting Data. R package version 2.16.0, 2015.
-
R package version 2.16.0, 2015
-
-
Warnes, G.R.1
Bolker, B.2
Bonebakker, L.3
Gentleman, R.4
-
43
-
-
84976556334
-
Heatplus: Heatmaps with row and/or column covariates and colored clusters
-
Ploner, A., Heatplus: Heatmaps with row and/or column covariates and colored clusters. R package version 2.13.0, 2014.
-
(2014)
R package version 2.13.0
-
-
Ploner, A.1
-
44
-
-
79956281509
-
A posteriori quality control for the curation and reuse of public proteomics data
-
Foster, J. M., Degroeve, S., Gatto, L., Visser, M. et al., A posteriori quality control for the curation and reuse of public proteomics data. Proteomics 2011, 11, 2182-2194.
-
(2011)
Proteomics
, vol.11
, pp. 2182-2194
-
-
Foster, J.M.1
Degroeve, S.2
Gatto, L.3
Visser, M.4
-
45
-
-
84886047856
-
corrplot: Visualization of a correlation matrix
-
Wei, T., corrplot: Visualization of a correlation matrix. R package version 0.73, 2013.
-
(2013)
R package version 0.73
-
-
Wei, T.1
-
46
-
-
85006422068
-
VennDiagram: Generate high-resolution Venn and Euler plots
-
Chen, H., VennDiagram: Generate high-resolution Venn and Euler plots. R package version 1.6.9, 2014.
-
(2014)
R package version 1.6.9
-
-
Chen, H.1
-
47
-
-
84926511189
-
Rgraphviz: Provides plotting capabilities for R graph objects
-
Hansen, K. D., Gentry, J., Long, L., Gentleman, R. et al., Rgraphviz: Provides plotting capabilities for R graph objects. R package version 2.11.0.
-
R package version 2.11.0
-
-
Hansen, K.D.1
Gentry, J.2
Long, L.3
Gentleman, R.4
-
48
-
-
85081865498
-
graph: A package to handle graph data structures
-
Gentleman, R., Whalen, E., Huber, W., Falcon, S., graph: A package to handle graph data structures. R package version 1.45.1, 2014.
-
(2014)
R package version 1.45.1
-
-
Gentleman, R.1
Whalen, E.2
Huber, W.3
Falcon, S.4
-
50
-
-
43349094507
-
The igraph software package for complex network research
-
Csardi, G., Nepusz, T., The igraph software package for complex network research. InterJournal Complex Systems, 2006, 1695.
-
(2006)
InterJournal Complex Systems
, vol.1695
-
-
Csardi, G.1
Nepusz, T.2
-
51
-
-
85081868833
-
rgl: 3D visualization device system (OpenGL)
-
Adler, D., Murdoch, D., Nenadic, O., Urbanek, S. et al., rgl: 3D visualization device system (OpenGL). R package version 0.95.1201, 2014.
-
(2014)
R package version 0.95.1201
-
-
Adler, D.1
Murdoch, D.2
Nenadic, O.3
Urbanek, S.4
-
52
-
-
84876725093
-
Animation: an r package for creating animations and demonstrating statistical methods
-
Xie, Y., Animation: an r package for creating animations and demonstrating statistical methods. J. Stat. Software 2013, 53, 1-27.
-
(2013)
J. Stat. Software
, vol.53
, pp. 1-27
-
-
Xie, Y.1
-
53
-
-
84867345063
-
A cross-platform toolkit for mass spectrometry and proteomics
-
Chambers, M. C., Maclean, B., Burke, R., Amodei, D. et al., A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 2012, 30, 918-920.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 918-920
-
-
Chambers, M.C.1
Maclean, B.2
Burke, R.3
Amodei, D.4
-
54
-
-
78651082595
-
mzml-a community standard for mass spectrometry data
-
2010
-
Martens, L., Chambers, M., Sturm, M., Kessner, D. et al., mzml-a community standard for mass spectrometry data. Mol. Cell. Proteomics 2010, doi 10.1074/mcp.R110.000133.
-
Mol. Cell. Proteomics
-
-
Martens, L.1
Chambers, M.2
Sturm, M.3
Kessner, D.4
-
55
-
-
8344284323
-
A common open representation of mass spectrometry data and its application to proteomics research
-
Pedrioli, P. G. A., Eng, J. K., Hubley, R., Vogelzang, M. et al., A common open representation of mass spectrometry data and its application to proteomics research. Nat. Biotechnol. 2004, 22, 1459-1466.
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 1459-1466
-
-
Pedrioli, P.G.A.1
Eng, J.K.2
Hubley, R.3
Vogelzang, M.4
-
56
-
-
85081864606
-
protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
-
Panse, C., Grossmann, J., Barkow-Oesterreicher, S., protViz: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics. R package version 0.2.9, 2014.
-
(2014)
R package version 0.2.9
-
-
Panse, C.1
Grossmann, J.2
Barkow-Oesterreicher, S.3
-
57
-
-
84865548780
-
MALDIquant: a versatile R package for the analysis of mass spectrometry data
-
Gibb, S., Strimmer, K., MALDIquant: a versatile R package for the analysis of mass spectrometry data. Bioinformatics 2012, 28, 2270-2271.
-
(2012)
Bioinformatics
, vol.28
, pp. 2270-2271
-
-
Gibb, S.1
Strimmer, K.2
-
58
-
-
32444446805
-
Xcms: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification
-
Smith, C. A., Want, E. J., O'Maille, G., Abagyan, R., Siuzdak, G., Xcms: processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching, and identification. Anal. Chem. 2006, 78, 779-787.
-
(2006)
Anal. Chem.
, vol.78
, pp. 779-787
-
-
Smith, C.A.1
Want, E.J.2
O'Maille, G.3
Abagyan, R.4
Siuzdak, G.5
-
59
-
-
33748659203
-
Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching
-
Du, P., Kibbe, W. A., Lin, S. M., Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching. Bioinformatics 2006, 22, 2059-2065.
-
(2006)
Bioinformatics
, vol.22
, pp. 2059-2065
-
-
Du, P.1
Kibbe, W.A.2
Lin, S.M.3
-
60
-
-
84862557848
-
An efficient method to calculate the aggregated isotopic distribution and exact center-masses
-
Claesen, J., Dittwald, P., Burzykowski, T., Valkenborg, D., An efficient method to calculate the aggregated isotopic distribution and exact center-masses. JASMS 2012, 23, 753-763.
-
(2012)
JASMS
, vol.23
, pp. 753-763
-
-
Claesen, J.1
Dittwald, P.2
Burzykowski, T.3
Valkenborg, D.4
-
61
-
-
84926511183
-
PROcess: Ciphergen SELDI-TOF Processing
-
Li, X., PROcess: Ciphergen SELDI-TOF Processing. R package version 1.43.0, 2005.
-
(2005)
R package version 1.43.0
-
-
Li, X.1
-
62
-
-
85081860907
-
proteoQC: An R package for proteomics data quality control
-
Wen, B., Gatto, L., proteoQC: An R package for proteomics data quality control. R package version 1.3.2., 2014.
-
(2014)
R package version 1.3.2.
-
-
Wen, B.1
Gatto, L.2
-
63
-
-
84865564453
-
ggbio: an R package for extending the grammar of graphics for genomic data
-
Yin, T., Cook, D., Lawrence, M., ggbio: an R package for extending the grammar of graphics for genomic data. Genome Biol. 2012, 13, R77.
-
(2012)
Genome Biol.
, vol.13
, pp. R77
-
-
Yin, T.1
Cook, D.2
Lawrence, M.3
-
64
-
-
84902087917
-
Gviz: Plotting data and annotation information along genomic coordinates
-
Hahne, F., Durinck, S., Ivanek, R., Mueller, A. et al. Gviz: Plotting data and annotation information along genomic coordinates. R package version 1.9.11.
-
R package version 1.9.11
-
-
Hahne, F.1
Durinck, S.2
Ivanek, R.3
Mueller, A.4
-
65
-
-
85081866612
-
Pviz: Peptide Annotation and Data Visualization using Gviz
-
Sauteraud, R., Jiang, M., Gottardo, R., Pviz: Peptide Annotation and Data Visualization using Gviz. R package version 0.99.0, 2014.
-
(2014)
R package version 0.99.0
-
-
Sauteraud, R.1
Jiang, M.2
Gottardo, R.3
-
66
-
-
85081868497
-
Pbase: Manipulating and exploring protein and proteomics data
-
Gatto, L., Gibb, S., Pbase: Manipulating and exploring protein and proteomics data. R package version 0.6.12, 2015.
-
(2015)
R package version 0.6.12
-
-
Gatto, L.1
Gibb, S.2
-
67
-
-
84859868686
-
The mzidentml data standard for mass spectrometry-based proteomics results
-
Jones, A. R., Eisenacher, M., Mayer, G., Kohlbacher, O. et al., The mzidentml data standard for mass spectrometry-based proteomics results. Mol. Cell Proteomics 2012, 11, M111.014381.
-
(2012)
Mol. Cell Proteomics
, vol.11
, pp. M111014381
-
-
Jones, A.R.1
Eisenacher, M.2
Mayer, G.3
Kohlbacher, O.4
-
69
-
-
85081864090
-
2015 Cardinal: Mass spectrometry imaging tools
-
Bemis, K. D., 2015 Cardinal: Mass spectrometry imaging tools. R package version 0.99.2, 2015.
-
(2015)
R package version 0.99.2
-
-
Bemis, K.D.1
-
70
-
-
33646236590
-
Mapping the arabidopsis organelle proteome
-
Dunkley, T. P. J., Hester, S., Shadforth, I. P., Runions, J. et al., Mapping the arabidopsis organelle proteome. Proc. Natl. Acad. Sci. USA 2006, 103, 6518-6523.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 6518-6523
-
-
Dunkley, T.P.J.1
Hester, S.2
Shadforth, I.P.3
Runions, J.4
-
71
-
-
33646473345
-
A mammalian organelle map by protein correlation profiling
-
Foster, L. J., Hoog, C. L. D., Zhang, Y., Zhang, Y. et al., A mammalian organelle map by protein correlation profiling. Cell 2006, 125, 187-199.
-
(2006)
Cell
, vol.125
, pp. 187-199
-
-
Foster, L.J.1
Hoog, C.L.D.2
Zhang, Y.3
Zhang, Y.4
-
72
-
-
78649680828
-
Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions
-
Trotter, M. W. B., Sadowski, P. G., Dunkley, T. P. J., Groen, A. J., Lilley, K. S., Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions. Proteomics 2010, 10, 4213-4219.
-
(2010)
Proteomics
, vol.10
, pp. 4213-4219
-
-
Trotter, M.W.B.1
Sadowski, P.G.2
Dunkley, T.P.J.3
Groen, A.J.4
Lilley, K.S.5
-
73
-
-
0019812922
-
A Short History of Tissue Fractionation
-
De Duve, C., Beaufay, H., A Short History of Tissue Fractionation. J. Cell Biol. 1981 91, 293s-299s.
-
(1981)
J. Cell Biol.
, vol.91
, pp. 293s-299s
-
-
De Duve, C.1
Beaufay, H.2
-
74
-
-
84893355890
-
The effect of organelle discovery upon sub-cellular protein localisation
-
Breckels, L. M., Gatto, L., Christoforou, A., Groen, A. J. et al., The effect of organelle discovery upon sub-cellular protein localisation. J. Proteomics 2013, 88, 129-140.
-
(2013)
J. Proteomics
, vol.88
, pp. 129-140
-
-
Breckels, L.M.1
Gatto, L.2
Christoforou, A.3
Groen, A.J.4
-
75
-
-
67049146295
-
Mapping organelle proteins and protein complexes in drosophila melanogaster
-
Tan, D. J., Dvinge, H., Christoforou, A., Bertone, P. et al., Mapping organelle proteins and protein complexes in drosophila melanogaster. J. Proteome Res. 2009, 8, 2667-2678.
-
(2009)
J. Proteome Res.
, vol.8
, pp. 2667-2678
-
-
Tan, D.J.1
Dvinge, H.2
Christoforou, A.3
Bertone, P.4
-
76
-
-
85081860234
-
interactiveDisplay: Package for enabling powerful shiny web displays of Bioconductor objects
-
Balcome, S., Carlson, M., interactiveDisplay: Package for enabling powerful shiny web displays of Bioconductor objects. R package version 1.3.9, 2014.
-
(2014)
R package version 1.3.9
-
-
Balcome, S.1
Carlson, M.2
-
78
-
-
85081865630
-
pRolocGUI: Interactive visualisation of organelle (spatial) proteomics data
-
Naake, T., Gatto, L. pRolocGUI: Interactive visualisation of organelle (spatial) proteomics data. R package version 0.99.7, 2014.
-
(2014)
R package version 0.99.7
-
-
Naake, T.1
Gatto, L.2
-
79
-
-
85081865096
-
rpx: R Interface to the ProteomeXchange Repository
-
Gatto, L., rpx: R Interface to the ProteomeXchange Repository. R package version 1.3.0, 2014.
-
(2014)
R package version 1.3.0
-
-
Gatto, L.1
-
80
-
-
84901599553
-
A draft map of the human proteome
-
Kim, M. S., Pinto, S. M., Getnet, D., Nirujogi, R. S. et al., A draft map of the human proteome. Nature 2014, 509, 575-581.
-
(2014)
Nature
, vol.509
, pp. 575-581
-
-
Kim, M.S.1
Pinto, S.M.2
Getnet, D.3
Nirujogi, R.S.4
-
81
-
-
29244477844
-
A human protein atlas for normal and cancer tissues based on antibody proteomics
-
Uhlén, M., Björling, E., Agaton, C., Szigyarto, C. A.-K. A. et al., A human protein atlas for normal and cancer tissues based on antibody proteomics. Mol. Cell. Proteomics 2005, 4, 1920-1932.
-
(2005)
Mol. Cell. Proteomics
, vol.4
, pp. 1920-1932
-
-
Uhlén, M.1
Björling, E.2
Agaton, C.3
Szigyarto, C.A.-K.A.4
-
82
-
-
78650034777
-
Towards a knowledge-based Human Protein Atlas
-
Uhlen, M., Oksvold, P., Fagerberg, L., Lundberg, E. et al., Towards a knowledge-based Human Protein Atlas. Nat. Biotechnol. 2010, 28, 1248-1250.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 1248-1250
-
-
Uhlen, M.1
Oksvold, P.2
Fagerberg, L.3
Lundberg, E.4
-
84
-
-
85051706927
-
UniProt.ws: R Interface to UniProt Web Services
-
Carlson, M., UniProt.ws: R Interface to UniProt Web Services. R package version 2.7.3.
-
R package version 2.7.3
-
-
Carlson, M.1
-
85
-
-
24044522270
-
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
-
Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S. et al., BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics 2005, 21, 3439-3440.
-
(2005)
Bioinformatics
, vol.21
, pp. 3439-3440
-
-
Durinck, S.1
Moreau, Y.2
Kasprzyk, A.3
Davis, S.4
-
86
-
-
68449101067
-
Mapping identifiers for the integration of genomic datasets with the r/bioconductor package biomart
-
Durinck, S., Spellman, P. T., Birney, E., Huber, W., Mapping identifiers for the integration of genomic datasets with the r/bioconductor package biomart. Nat. Protoc. 2009, 4, 1184-1191.
-
(2009)
Nat. Protoc.
, vol.4
, pp. 1184-1191
-
-
Durinck, S.1
Spellman, P.T.2
Birney, E.3
Huber, W.4
-
87
-
-
85081860841
-
PSICQUIC: Protemics Standard Initiative Common QUery InterfaCe
-
Shannon, P., PSICQUIC: Protemics Standard Initiative Common QUery InterfaCe. R package version 1.5.5, 2015.
-
(2015)
R package version 1.5.5
-
-
Shannon, P.1
-
88
-
-
68549090980
-
Importing ArrayExpress datasets into R/Bioconductor
-
Kauffmann, A., Rayner, T. F., Parkinson, H., Kapushesky, M. et al., Importing ArrayExpress datasets into R/Bioconductor. Bioinformatics 2009, 25, 2092-2094.
-
(2009)
Bioinformatics
, vol.25
, pp. 2092-2094
-
-
Kauffmann, A.1
Rayner, T.F.2
Parkinson, H.3
Kapushesky, M.4
-
89
-
-
34547871639
-
GEOquery: a bridge between the gene expression omnibus (GEO) and bioconductor
-
Davis, S., Meltzer, P., GEOquery: a bridge between the gene expression omnibus (GEO) and bioconductor. Bioinformatics 2007, 14, 1846-1847.
-
(2007)
Bioinformatics
, vol.14
, pp. 1846-1847
-
-
Davis, S.1
Meltzer, P.2
-
90
-
-
84872274753
-
SRAdb: query and use public next-generation sequencing data from within r
-
Zhu, Y., Stephens, R. M., Meltzer, P. S., Davis, S. R., SRAdb: query and use public next-generation sequencing data from within r. BMC Bioinformatics 2013, 14, 19.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 19
-
-
Zhu, Y.1
Stephens, R.M.2
Meltzer, P.S.3
Davis, S.R.4
-
91
-
-
0034069495
-
Gene ontology: tool for the unification of biology. the gene ontology consortium
-
Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D. et al., Gene ontology: tool for the unification of biology. the gene ontology consortium. Nat. Genet. 2000, 25, 25-29.
-
(2000)
Nat. Genet.
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.A.2
Blake, J.A.3
Botstein, D.4
-
92
-
-
33846689706
-
Using GOstats to test gene lists for GO term association
-
Falcon, S., Gentleman, R., Using GOstats to test gene lists for GO term association. Bioinformatics 2007, 23, 257-258.
-
(2007)
Bioinformatics
, vol.23
, pp. 257-258
-
-
Falcon, S.1
Gentleman, R.2
-
93
-
-
67649202800
-
GAGE: generally applicable gene set enrichment for pathway analysis
-
Luo, W., Friedman, M. S., Shedden, K., Hankenson, K. D., Woolf, P. J., GAGE: generally applicable gene set enrichment for pathway analysis. BMC Bioinformatics 2009, 10, 161.
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 161
-
-
Luo, W.1
Friedman, M.S.2
Shedden, K.3
Hankenson, K.D.4
Woolf, P.J.5
-
94
-
-
84926511170
-
SPIA: Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations
-
Tarca, A. L., Kathri, P., Draghici, S., SPIA: Signaling Pathway Impact Analysis (SPIA) using combined evidence of pathway over-representation and unusual signaling perturbations. R package version 2.19.0, 2013.
-
(2013)
R package version 2.19.0
-
-
Tarca, A.L.1
Kathri, P.2
Draghici, S.3
-
95
-
-
0021425467
-
Literate programming
-
Knuth, D. E., Literate programming. Comp. J. 1984, 27, 91-111.
-
(1984)
Comp. J.
, vol.27
, pp. 91-111
-
-
Knuth, D.E.1
-
96
-
-
77956633623
-
An invitation to reproducible computational research
-
Donoho, D. L., An invitation to reproducible computational research. Biostatistics 2010, 11, 385-388.
-
(2010)
Biostatistics
, vol.11
, pp. 385-388
-
-
Donoho, D.L.1
-
97
-
-
18544387899
-
Reproducible research: a bioinformatics case study
-
Gentleman, R., Reproducible research: a bioinformatics case study. Stat. Appl. Genet. Mol. Biol. 2005, 4.
-
(2005)
Stat. Appl. Genet. Mol. Biol.
, vol.4
-
-
Gentleman, R.1
-
98
-
-
70149102312
-
Reproducible research and biostatistics
-
Peng, R. D., Reproducible research and biostatistics. Biostatistics 2009, 10, 405-408.
-
(2009)
Biostatistics
, vol.10
, pp. 405-408
-
-
Peng, R.D.1
-
99
-
-
82755174123
-
Reproducible research in computational science
-
Peng, R. D., Reproducible research in computational science. Science 2011, 334, 1226-1227.
-
(2011)
Science
, vol.334
, pp. 1226-1227
-
-
Peng, R.D.1
-
100
-
-
0242529706
-
Sweave: Dynamic Generation of Statistical Reports Using Literate Data Analysis
-
in: Härdle, W., Rönz, B. (Eds.), Physica Verlag, Heidelberg, Germany .
-
Leisch, F., Sweave: Dynamic Generation of Statistical Reports Using Literate Data Analysis, in: Härdle, W., Rönz, B. (Eds.), Compstat 2002, Proceedings in Computational Statistics, Physica Verlag, Heidelberg, Germany 2002.
-
(2002)
Compstat 2002, Proceedings in Computational Statistics
-
-
Leisch, F.1
-
102
-
-
84876702088
-
knitr: A General-Purpose Package for Dynamic Report Generation in R
-
Xie, Y., knitr: A General-Purpose Package for Dynamic Report Generation in R. R package version 1.9, 2015.
-
(2015)
R package version 1.9
-
-
Xie, Y.1
-
103
-
-
85081866351
-
qcmetrics: A Framework for Quality Control
-
Gatto, L., qcmetrics: A Framework for Quality Control. R package version 1.5.1, 2014.
-
(2014)
R package version 1.5.1
-
-
Gatto, L.1
|