{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,27]],"date-time":"2026-03-27T02:40:15Z","timestamp":1774579215297,"version":"3.50.1"},"publisher-location":"New York, NY","reference-count":72,"publisher":"Springer New York","isbn-type":[{"value":"9781493935703","type":"print"},{"value":"9781493935727","type":"electronic"}],"license":[{"start":{"date-parts":[[2016,1,1]],"date-time":"2016-01-01T00:00:00Z","timestamp":1451606400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016]]},"DOI":"10.1007\/978-1-4939-3572-7_12","type":"book-chapter","created":{"date-parts":[[2016,4,26]],"date-time":"2016-04-26T10:25:17Z","timestamp":1461666317000},"page":"225-243","source":"Crossref","is-referenced-by-count":11,"title":["Promises and Pitfalls of High-Throughput Biological Assays"],"prefix":"10.1007","author":[{"given":"Greg","family":"Finak","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Raphael","family":"Gottardo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,4,27]]},"reference":[{"key":"12_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/biostatistics\/kxt007","volume":"15","author":"LR Jager","year":"2014","unstructured":"Jager LR, Leek JT (2014) An estimate of the science-wise false discovery rate and application to the top medical literature. Biostatistics 15:1\u201312","journal-title":"Biostatistics"},{"key":"12_CR2","doi-asserted-by":"publisher","first-page":"e124","DOI":"10.1371\/journal.pmed.0020124","volume":"2","author":"JPA Ioannidis","year":"2005","unstructured":"Ioannidis JPA (2005) Why most published research findings are false. PLoS Med 2:e124","journal-title":"PLoS Med"},{"key":"12_CR3","doi-asserted-by":"publisher","first-page":"867","DOI":"10.1016\/0140-6736(91)90201-Y","volume":"337","author":"PJ Easterbrook","year":"1991","unstructured":"Easterbrook PJ, Berlin JA, Gopalan R, Matthews DR (1991) Publication bias in clinical research. Lancet 337:867\u2013872","journal-title":"Lancet"},{"key":"12_CR4","doi-asserted-by":"publisher","first-page":"e168","DOI":"10.1371\/journal.pmed.0040168","volume":"4","author":"S Goodman","year":"2007","unstructured":"Goodman S, Greenland S (2007) Why most published research findings are false: problems in the analysis. PLoS Med 4:e168","journal-title":"PLoS Med"},{"key":"12_CR5","doi-asserted-by":"publisher","first-page":"868","DOI":"10.1136\/bmj.329.7471.868","volume":"329","author":"E Elm von","year":"2004","unstructured":"von Elm E, Egger M (2004) The scandal of poor epidemiological research. BMJ 329:868\u2013869","journal-title":"BMJ"},{"key":"12_CR6","doi-asserted-by":"publisher","first-page":"273","DOI":"10.7326\/0003-4819-137-4-200208200-00012","volume":"137","author":"LL Humphrey","year":"2002","unstructured":"Humphrey LL, Chan BKS, Sox HC (2002) Postmenopausal hormone replacement therapy and the primary prevention of cardiovascular disease. Ann Intern Med 137:273\u2013284","journal-title":"Ann Intern Med"},{"key":"12_CR7","doi-asserted-by":"publisher","first-page":"883","DOI":"10.1136\/bmj.38250.571088.55","volume":"329","author":"SJ Pocock","year":"2004","unstructured":"Pocock SJ, Collier TJ, Dandreo KJ, de Stavola BL, Goldman MB, Kalish LA et al (2004) Issues in the reporting of epidemiological studies: a survey of recent practice. BMJ 329:883","journal-title":"BMJ"},{"key":"12_CR8","doi-asserted-by":"publisher","first-page":"618","DOI":"10.1038\/nm0610-618a","volume":"16","author":"S Hutson","year":"2010","unstructured":"Hutson S (2010) Data handling errors spur debate over clinical trial. Nat Med 16:618","journal-title":"Nat Med"},{"key":"12_CR9","doi-asserted-by":"publisher","first-page":"688","DOI":"10.1373\/clinchem.2010.158618","volume":"57","author":"KA Baggerly","year":"2011","unstructured":"Baggerly KA, Coombes KR (2011) What information should be required to support clinical \u201comics\u201d publications? Clin Chem 57:688\u2013690","journal-title":"Clin Chem"},{"key":"12_CR10","doi-asserted-by":"publisher","first-page":"1226","DOI":"10.1126\/science.1213847","volume":"334","author":"RD Peng","year":"2011","unstructured":"Peng RD (2011) Reproducible research in computational science. Science 334:1226\u20131227","journal-title":"Science"},{"key":"12_CR11","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1038\/ng.295","volume":"41","author":"JPA Ioannidis","year":"2009","unstructured":"Ioannidis JPA, Allison DB, Ball CA, Coulibaly I, Cui X, Culhane AC et al (2009) Repeatability of published microarray gene expression analyses. Nat Genet 41:149\u2013155","journal-title":"Nat Genet"},{"key":"12_CR12","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1038\/487427a","volume":"487","author":"D Macarthur","year":"2012","unstructured":"Macarthur D (2012) Methods: face up to false positives. Nature 487:427\u2013428","journal-title":"Nature"},{"key":"12_CR13","doi-asserted-by":"publisher","first-page":"404","DOI":"10.1126\/science.333.6041.404-a","volume":"333","author":"P Sebastiani","year":"2011","unstructured":"Sebastiani P, Solovieff N, Puca A, Hartley SW, Melista E, Andersen S et al (2011) Retraction. Science 333:404","journal-title":"Science"},{"key":"12_CR14","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1038\/ng.1037","volume":"44","author":"KA Hunt","year":"2012","unstructured":"Hunt KA, Smyth DJ, Balschun T, Ban M, Mistry V, Ahmad T et al (2012) Rare and functional SIAE variants are not associated with autoimmune disease risk in up to 66,924 individuals of European ancestry. Nat Genet 44:3\u20135","journal-title":"Nat Genet"},{"key":"12_CR15","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1093\/biostatistics\/kxp014","volume":"10","author":"RD Peng","year":"2009","unstructured":"Peng RD (2009) Reproducible research and biostatistics. Biostatistics 10:405\u2013408","journal-title":"Biostatistics"},{"key":"12_CR16","doi-asserted-by":"publisher","first-page":"679","DOI":"10.1126\/science.aaa1724","volume":"346","author":"M McNutt","year":"2014","unstructured":"McNutt M (2014) Journals unite for reproducibility. Science 346:679","journal-title":"Science"},{"key":"12_CR17","unstructured":"Principles and Guidelines for Reporting Preclinical Research\u2014About NIH\u2014National Institutes of Health (NIH) [Internet]. [cited 10 Sep 2015]. http:\/\/www.nih.gov\/about\/reporting-preclinical-research.htm"},{"key":"12_CR18","doi-asserted-by":"publisher","first-page":"1135","DOI":"10.1038\/nbt1209-1135","volume":"27","author":"WS Noble","year":"2009","unstructured":"Noble WS (2009) How does multiple testing correction work? Nat Biotechnol 27:1135\u20131137","journal-title":"Nat Biotechnol"},{"key":"12_CR19","doi-asserted-by":"publisher","first-page":"479","DOI":"10.1111\/1467-9868.00346","volume":"64","author":"JD Storey","year":"2002","unstructured":"Storey JD (2002) A direct approach to false discovery rates. J R Stat Soc B Stat Methodol 64:479\u2013498","journal-title":"J R Stat Soc B Stat Methodol"},{"key":"12_CR20","doi-asserted-by":"publisher","first-page":"800","DOI":"10.1093\/biomet\/75.4.800","volume":"75","author":"Y Hochberg","year":"1988","unstructured":"Hochberg Y (1988) A sharper Bonferroni procedure for multiple tests of significance. Biometrika 75:800\u2013802","journal-title":"Biometrika"},{"key":"12_CR21","doi-asserted-by":"publisher","first-page":"383","DOI":"10.1093\/biomet\/75.2.383","volume":"75","author":"G Hommel","year":"1988","unstructured":"Hommel G (1988) A stagewise rejective multiple test procedure based on a modified Bonferroni test. Biometrika 75:383\u2013386","journal-title":"Biometrika"},{"key":"12_CR22","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc B Stat Methodol 57:289\u2013300","journal-title":"J R Stat Soc B Stat Methodol"},{"key":"12_CR23","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1016\/S0378-3758(99)00041-5","volume":"82","author":"D Yekutieli","year":"1999","unstructured":"Yekutieli D, Benjamini Y (1999) Resampling-based false discovery rate controlling multiple test procedures for correlated test statistics. J Stat Plan Infer 82:171\u2013196","journal-title":"J Stat Plan Infer"},{"key":"12_CR24","first-page":"65","volume":"6","author":"S Holm","year":"1979","unstructured":"Holm S (1979) A simple sequentially rejective multiple test procedure. Scand Stat Theory Appl 6:65\u201370","journal-title":"Scand Stat Theory Appl"},{"key":"12_CR25","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1214\/ss\/1056397487","volume":"18","author":"S Dudoit","year":"2003","unstructured":"Dudoit S, Shaffer JP, Boldrick JC (2003) Multiple hypothesis testing in microarray experiments. Stat Sci 18:71\u2013103","journal-title":"Stat Sci"},{"key":"12_CR26","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1146\/annurev.ps.46.020195.003021","volume":"46","author":"JP Shaffer","year":"1995","unstructured":"Shaffer JP (1995) Multiple hypothesis testing. Annu Rev Psychol 46:561\u2013584","journal-title":"Annu Rev Psychol"},{"key":"12_CR27","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1214\/aos\/1028144846","volume":"26","author":"SK Sarkar","year":"1998","unstructured":"Sarkar SK (1998) Some probability inequalities for ordered MTP2 random variables: a proof of the Simes conjecture. Ann Stat 26:494\u2013504","journal-title":"Ann Stat"},{"key":"12_CR28","doi-asserted-by":"publisher","first-page":"1601","DOI":"10.1080\/01621459.1997.10473682","volume":"92","author":"SK Sarkar","year":"1997","unstructured":"Sarkar SK, Chang C-K (1997) The Simes method for multiple hypothesis testing with positively dependent test statistics. J Am Stat Assoc 92:1601\u20131608","journal-title":"J Am Stat Assoc"},{"key":"12_CR29","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.2307\/2532694","volume":"48","author":"SP Wright","year":"1992","unstructured":"Wright SP (1992) Adjusted P-values for simultaneous inference. Biometrics 48:1005\u20131013","journal-title":"Biometrics"},{"key":"12_CR30","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1080\/10618600.1996.10474713","volume":"5","author":"R Ihaka","year":"1996","unstructured":"Ihaka R, Gentleman R (1996) R: a language for data analysis and graphics. J Comput Graph Stat 5:299\u2013314","journal-title":"J Comput Graph Stat"},{"key":"12_CR31","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1038\/nrg2825","volume":"11","author":"JT Leek","year":"2010","unstructured":"Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE et al (2010) Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet 11:733\u2013739","journal-title":"Nat Rev Genet"},{"key":"12_CR32","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1038\/ng1201-365","volume":"29","author":"A Brazma","year":"2001","unstructured":"Brazma A, Hingamp P, Quackenbush J, Sherlock G, Spellman P, Stoeckert C et al (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365\u2013371","journal-title":"Nat Genet"},{"key":"12_CR33","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1002\/cyto.a.20623","volume":"73","author":"JA Lee","year":"2008","unstructured":"Lee JA, Spidlen J, Boyce K, Cai J, Crosbie N, Dalphin M et al (2008) MIFlowCyt: the minimum information about a flow cytometry experiment. Cytometry A 73:926\u2013930","journal-title":"Cytometry A"},{"key":"12_CR34","unstructured":"The Functional Genomics Data Society. Minimum Information about a high-throughput SeQuencing Experiment\u2014MINSEQE (Draft Proposal) [Internet]. http:\/\/www.mged.org\/minseqe\/"},{"key":"12_CR35","doi-asserted-by":"crossref","first-page":"126","DOI":"10.2307\/20168137","volume":"78","author":"L Thomas","year":"1997","unstructured":"Thomas L, Krebs CJ (1997) A review of statistical power analysis software. Bull Ecol Soc Am 78:126\u2013138","journal-title":"Bull Ecol Soc Am"},{"key":"12_CR36","unstructured":"Champely S (2009) pwr: basic functions for power analysis. R package version 1.1. 1. The R Foundation, Vienna, Austria"},{"key":"12_CR37","volume-title":"Sources and solutions","author":"A Scherer","year":"2009","unstructured":"Scherer A (2009) Sources and solutions. Wiley, Chichester"},{"key":"12_CR38","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1093\/biostatistics\/kxj037","volume":"8","author":"WE Johnson","year":"2007","unstructured":"Johnson WE, Li C, Rabinovic A (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics 8:118\u2013127","journal-title":"Biostatistics"},{"key":"12_CR39","doi-asserted-by":"publisher","first-page":"e17238","DOI":"10.1371\/journal.pone.0017238","volume":"6","author":"C Chen","year":"2011","unstructured":"Chen C, Grennan K, Badner J, Zhang D, Gershon E, Jin L et al (2011) Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods. PLoS One 6:e17238","journal-title":"PLoS One"},{"key":"12_CR40","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1002\/cyto.a.20823","volume":"77","author":"F Hahne","year":"2010","unstructured":"Hahne F, Khodabakhshi AH, Bashashati A, Wong C-J, Gascoyne RD, Weng AP et al (2010) Per-channel basis normalization methods for flow cytometry data. Cytometry A 77:121\u2013131","journal-title":"Cytometry A"},{"key":"12_CR41","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1002\/cyto.a.22433","volume":"85","author":"G Finak","year":"2014","unstructured":"Finak G, Jiang W, Krouse K, Wei C, Sanz I, Phippard D et al (2014) High-throughput flow cytometry data normalization for clinical trials. Cytometry A 85:277\u2013286","journal-title":"Cytometry A"},{"key":"12_CR42","doi-asserted-by":"publisher","first-page":"921","DOI":"10.1093\/bioinformatics\/bts055","volume":"28","author":"DC Jones","year":"2012","unstructured":"Jones DC, Ruzzo WL, Peng X, Katze MG (2012) A new approach to bias correction in RNA-Seq. Bioinformatics 28:921\u2013928","journal-title":"Bioinformatics"},{"key":"12_CR43","volume-title":"Models, methods, and applications","author":"JP Buonaccorsi","year":"2009","unstructured":"Buonaccorsi JP (2009) Models, methods, and applications. Chapman & Hall\/CRC, New York"},{"key":"12_CR44","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1186\/1471-2172-6-13","volume":"6","author":"HT Maecker","year":"2005","unstructured":"Maecker HT, Rinfret A, D\u2019Souza P, Darden J, Roig E, Landry C et al (2005) Standardization of cytokine flow cytometry assays. BMC Immunol 6:13","journal-title":"BMC Immunol"},{"issue":"28","key":"12_CR45","doi-asserted-by":"publisher","first-page":"3748","DOI":"10.1002\/sim.5446","volume":"31","author":"Y Huang","year":"2012","unstructured":"Huang Y, Moodie Z, Li S, Self SG (2012) Comparing and combining assay measurements across laboratories via integration of paired-sample data to correct for measurement error. Stat Med 31(28):3748\u20133759","journal-title":"Stat Med"},{"key":"12_CR46","unstructured":"Bland JM, Altman DG (1986) Statistical methods for assessing agreement between two methods of clinical measurement. Report No.: 0140-6736 (Print)r0140-6736 (Linking). pp 307\u2013310"},{"key":"12_CR47","first-page":"111","volume":"12","author":"S Dudoit","year":"2002","unstructured":"Dudoit S, Yang YH, Callow MJ, Speed TP (2002) Statistical methods for identifying differentially expressed genes in replicated cDNA microarray experiments. Stat Sin 12:111\u2013140","journal-title":"Stat Sin"},{"key":"12_CR48","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1038\/nri3158","volume":"12","author":"HT Maecker","year":"2012","unstructured":"Maecker HT, McCoy JP, Nussenblatt R (2012) Standardizing immunophenotyping for the Human Immunology Project. Nat Rev Immunol 12:191\u2013200","journal-title":"Nat Rev Immunol"},{"key":"12_CR49","unstructured":"Finak G, Langweiler M, Malekesmaeili M, Stanton R, Ramey J, Jaimes M et al (2014) Standardizing flow cytometry immunophenotyping: automated gating recapitulates central manual analysis with low variability. Cyto 2014. p Parallel Session 17\u2013Flow Cytometry Data Analysis"},{"key":"12_CR50","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1093\/bioinformatics\/btp616","volume":"26","author":"MD Robinson","year":"2010","unstructured":"Robinson MD, McCarthy DJ, Smyth GK (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139\u2013140","journal-title":"Bioinformatics"},{"key":"12_CR51","unstructured":"Anders S, Huber W (2012) Differential expression of RNA-Seq data at the gene level\u2014the DESeq package"},{"key":"12_CR52","doi-asserted-by":"publisher","first-page":"461","DOI":"10.1093\/bioinformatics\/bts714","volume":"29","author":"A McDavid","year":"2013","unstructured":"McDavid A, Finak G, Chattopadyay PK, Dominguez M, Lamoreaux L, Ma SS et al (2013) Data exploration, quality control and testing in single-cell qPCR-based gene expression experiments. Bioinformatics 29:461\u2013467","journal-title":"Bioinformatics"},{"key":"12_CR53","doi-asserted-by":"publisher","first-page":"e1003696","DOI":"10.1371\/journal.pcbi.1003696","volume":"10","author":"A McDavid","year":"2014","unstructured":"McDavid A, Dennis L, Danaher P, Finak G, Krouse M, Wang A et al (2014) Modeling bi-modality improves characterization of cell cycle on gene expression in single cells. PLoS Comput Biol 10:e1003696","journal-title":"PLoS Comput Biol"},{"key":"12_CR54","doi-asserted-by":"crossref","unstructured":"Hicks SC, Teng M, Irizarry RA (2015) On the widespread and critical impact of systematic bias and batch effects in single-cell RNA-Seq data. bioRxiv. http:\/\/dx.doi.org\/10.1101\/025528","DOI":"10.1101\/025528"},{"key":"12_CR55","doi-asserted-by":"publisher","first-page":"278","DOI":"10.1186\/s13059-015-0844-5","volume":"16","author":"G Finak","year":"2015","unstructured":"Finak G, McDavid A, Yajima M, Deng J, Gersuk V, Shalek AK et al (2015) MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA-seq data. Genome Biol 16:278","journal-title":"Genome Biol"},{"key":"12_CR56","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1038\/nature13235","volume":"510","author":"AK Shalek","year":"2014","unstructured":"Shalek AK, Satija R, Shuga J, Trombetta JJ, Gennert D, Lu D et al (2014) Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature 510:263\u2013269","journal-title":"Nature"},{"key":"12_CR57","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.jim.2013.06.001","volume":"395","author":"GC Imholte","year":"2013","unstructured":"Imholte GC, Sauteraud R, Korber B, Bailer RT, Turk ET, Shen X et al (2013) A computational framework for the analysis of peptide microarray antibody binding data with application to HIV vaccine profiling. J Immunol Methods 395:1\u201313","journal-title":"J Immunol Methods"},{"key":"12_CR58","doi-asserted-by":"publisher","first-page":"e1003806","DOI":"10.1371\/journal.pcbi.1003806","volume":"10","author":"G Finak","year":"2014","unstructured":"Finak G, Frelinger J, Jiang W, Newell EW, Ramey J, Davis MM et al (2014) OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis. PLoS Comput Biol 10:e1003806","journal-title":"PLoS Comput Biol"},{"key":"12_CR59","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1186\/1471-2105-10-106","volume":"10","author":"F Hahne","year":"2009","unstructured":"Hahne F, LeMeur N, Brinkman RR, Ellis B, Haaland P, Sarkar D et al (2009) flowCore: a Bioconductor package for high throughput flow cytometry. BMC Bioinformatics 10:106","journal-title":"BMC Bioinformatics"},{"key":"12_CR60","doi-asserted-by":"publisher","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"RC Gentleman","year":"2004","unstructured":"Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S et al (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5:R80","journal-title":"Genome Biol"},{"key":"12_CR61","doi-asserted-by":"publisher","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","volume":"25","author":"PJA Cock","year":"2009","unstructured":"Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A et al (2009) Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 25:1422\u20131423","journal-title":"Bioinformatics"},{"key":"12_CR62","doi-asserted-by":"publisher","first-page":"1611","DOI":"10.1101\/gr.361602","volume":"12","author":"JE Stajich","year":"2002","unstructured":"Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C et al (2002) The Bioperl toolkit: Perl modules for the life sciences. Genome Res 12:1611\u20131618","journal-title":"Genome Res"},{"key":"12_CR63","doi-asserted-by":"publisher","first-page":"500","DOI":"10.1038\/ng0506-500","volume":"38","author":"M Reich","year":"2006","unstructured":"Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP (2006) GenePattern 2.0. Nat Genet 38:500\u2013501","journal-title":"Nat Genet"},{"key":"12_CR64","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/1751-0473-8-14","volume":"8","author":"J Spidlen","year":"2013","unstructured":"Spidlen J, Barsky A, Breuer K, Carr P, Nazaire M-D, Hill BA et al (2013) GenePattern flow cytometry suite. Source Code Biol Med 8:14","journal-title":"Source Code Biol Med"},{"key":"12_CR65","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1186\/1471-2105-12-71","volume":"12","author":"EK Nelson","year":"2011","unstructured":"Nelson EK, Piehler B, Eckels J, Rauch A, Bellew M, Hussey P et al (2011) LabKey Server: an open source platform for scientific data integration, analysis and collaboration. BMC Bioinformatics 12:71","journal-title":"BMC Bioinformatics"},{"key":"12_CR66","doi-asserted-by":"publisher","first-page":"146","DOI":"10.1038\/nbt.2777","volume":"32","author":"V Brusic","year":"2014","unstructured":"Brusic V, Gottardo R, Kleinstein SH, Davis MM, HIPC Steering Committee (2014) Computational resources for high-dimensional immune analysis from the Human Immunology Project Consortium. Nat Biotechnol 32:146\u2013148","journal-title":"Nat Biotechnol"},{"key":"12_CR67","doi-asserted-by":"publisher","first-page":"e1428","DOI":"10.7717\/peerj.1273","volume":"3","author":"P Tommaso Di","year":"2015","unstructured":"Di Tommaso P, Palumbo E, Chatzou M, Prieto P, Heuer ML, Notredame C (2015) The impact of Docker containers on the performance of genomic pipelines. PeerJ 3:e1428","journal-title":"PeerJ"},{"key":"12_CR68","unstructured":"Boettiger C (2014) An introduction to Docker for reproducible research, with examples from the R environment. arXiv [cs.SE]"},{"key":"12_CR69","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1126\/science.1179653","volume":"327","author":"JP Mesirov","year":"2010","unstructured":"Mesirov JP (2010) Accessible reproducible research. Science 327:415\u2013416","journal-title":"Science"},{"key":"12_CR70","first-page":"28","volume":"2","author":"F Leisch","year":"2002","unstructured":"Leisch F (2002) Sweave, Part I: Mixing R and LaTeX. R News 2:28\u201331","journal-title":"R News"},{"key":"12_CR71","unstructured":"Gentleman R, Lang DT (2004) Statistical analyses and reproducible research. Available at: http:\/\/biostats.bepress.com\/bioconductor\/paper2\/"},{"key":"12_CR72","unstructured":"Allaire J, Cheng J, Xie Y, McPherson J, Chang W, Allen J et al (2015) rmarkdown: dynamic documents for R. R package version 0.5"}],"container-title":["Methods in Molecular Biology","Data Mining Techniques for the Life Sciences"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-4939-3572-7_12","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,15]],"date-time":"2024-06-15T23:50:23Z","timestamp":1718495423000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-1-4939-3572-7_12"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016]]},"ISBN":["9781493935703","9781493935727"],"references-count":72,"URL":"https:\/\/doi.org\/10.1007\/978-1-4939-3572-7_12","relation":{},"ISSN":["1064-3745","1940-6029"],"issn-type":[{"value":"1064-3745","type":"print"},{"value":"1940-6029","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016]]}}}