-
1
-
-
77958471357
-
Differential expression analysis for sequence count data
-
Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biology 11(10):R106 DOI 10.1186/gb-2010-11-10-r106.
-
(2010)
Genome Biology
, vol.11
, Issue.10
, pp. R106
-
-
Anders, S.1
Huber, W.2
-
2
-
-
0001677717
-
Controlling the false discovery rate: a practical and powerful approach to multiple testing.
-
Benjamini Y, Hochberg Y. 1995. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Proceedings of the Royal Statistical Society Series B 57:289-300.
-
(1995)
Proceedings of the Royal Statistical Society Series B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
3
-
-
79953034289
-
Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-seq and microarrays.
-
Bottomly D, Walter NAR, Hunter JE, Darakjian P, Kawane S, Buck KJ, Searles RP, Mooney M, McWeeney SK, Hitzemann R. 2011. Evaluating gene expression in C57BL/6J and DBA/2J mouse striatum using RNA-seq and microarrays. PLoS ONE 6:e17820 DOI 10.1371/journal.pone.0017820.
-
(2011)
PLoS ONE
, vol.6
-
-
Bottomly, D.1
Walter, N.A.R.2
Hunter, J.E.3
Darakjian, P.4
Kawane, S.5
Buck, K.J.6
Searles, R.P.7
Mooney, M.8
McWeeney, S.K.9
Hitzemann, R.10
-
4
-
-
84887791432
-
A comprehensive evaluation of normalization methods for illumina high-throughput RNA sequencing data analysis.
-
Dillies M-A, Rau A, Aubert J, Hennequet-Antier C, Jeanmougin M, Servant N, Keime C, Marot G, Castel D, Estelle J, Guernec G, Jagla B, Jouneau L, Laloë D, Le Gall C, Schaëffer B, Le CromS, Guedj M, Jaffrézic F. 2013. A comprehensive evaluation of normalization methods for illumina high-throughput RNA sequencing data analysis. Briefings in Bioinformatics 14:671-683 DOI 10.1093/bib/bbs046.
-
(2013)
Briefings in Bioinformatics
, vol.14
, pp. 671-683
-
-
Dillies, M.-A.1
Rau, A.2
Aubert, J.3
Hennequet-Antier, C.4
Jeanmougin, M.5
Servant, N.6
Keime, C.7
Marot, G.8
Castel, D.9
Estelle, J.10
Guernec, G.11
Jagla, B.12
Jouneau, L.13
Laloë, D.14
Le Gall, C.15
Schaëffer, B.16
Le, CromS.17
Guedj, M.18
Jaffrézic, F.19
-
5
-
-
0007231012
-
Two-sided P-values from discrete asymmetric distributions based on uniformly most powerful unbiased tests
-
Dunne A, Pawitan Y, Doody L. 1996. Two-sided P-values from discrete asymmetric distributions based on uniformly most powerful unbiased tests. The Statistician 45(4):397-405 DOI 10.2307/2988542.
-
(1996)
The Statistician
, vol.45
, Issue.4
, pp. 397-405
-
-
Dunne, A.1
Pawitan, Y.2
Doody, L.3
-
6
-
-
2142732441
-
Large-scale simultaneous hypothesis testing: the choice of a null hypothesis
-
Efron B. 2004. Large-scale simultaneous hypothesis testing: the choice of a null hypothesis. Journal of the American Statistical Association 99(465):96-104 DOI 10.1198/016214504000000089.
-
(2004)
Journal of the American Statistical Association
, vol.99
, Issue.465
, pp. 96-104
-
-
Efron, B.1
-
7
-
-
84882359581
-
A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments.
-
Esnaola M, Puig P, Gonzalez D, Castelo R, Gonzalez JR. 2013. A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments. BMC Bioinformatics 14:254 DOI 10.1186/1471-2105-14-254.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 254
-
-
Esnaola, M.1
Puig, P.2
Gonzalez, D.3
Castelo, R.4
Gonzalez, J.R.5
-
8
-
-
34250721552
-
Estimating the null and the proportion of nonnull effects in large-scale multiple comparisons.
-
Jin J, Cai T. 2007. Estimating the null and the proportion of nonnull effects in large-scale multiple comparisons. Journal of the American Statistical Association 102:495-506 DOI 10.1198/016214507000000167.
-
(2007)
Journal of the American Statistical Association
, vol.102
, pp. 495-506
-
-
Jin, J.1
Cai, T.2
-
9
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short dna sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short dna sequences to the human genome. Genome Biology 10(3):R25 DOI 10.1186/gb-2009-10-3-r25.
-
(2009)
Genome Biology
, vol.10
, Issue.3
, pp. R25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
10
-
-
84863562292
-
Normalization, testing, and false discovery rate estimation for RNA-sequencing data
-
Li J, Witten D, Johnstone I, Tibshirani R. 2012. Normalization, testing, and false discovery rate estimation for RNA-sequencing data. Biostatistics 13(3):523-538 DOI 10.1093/biostatistics/kxr031.
-
(2012)
Biostatistics
, vol.13
, Issue.3
, pp. 523-538
-
-
Li, J.1
Witten, D.2
Johnstone, I.3
Tibshirani, R.4
-
11
-
-
84908535418
-
Differential analysis of count data-the DESeq2 package.
-
Love M, Anders S, Huber W. 2013. Differential analysis of count data-the DESeq2 package. Available at http://www.bioconductor.org/packages/2.13/bioc/vignettes/deseq2/inst/doc/des.pdf.
-
(2013)
-
-
Love, M.1
Anders, S.2
Huber, W.3
-
12
-
-
84879198972
-
Detecting differential expression in RNAsequence data using quasi-likelihood with shrunken dispersion estimates
-
Lund S, Nettleton D, McCarthy D, Smyth G. 2012. Detecting differential expression in RNAsequence data using quasi-likelihood with shrunken dispersion estimates. Statistical Applications in Genetics and Molecular Biology 11(5): Article 8 DOI 10.1515/1544-6115.1826.
-
(2012)
Statistical Applications in Genetics and Molecular Biology
, vol.11
, Issue.5
-
-
Lund, S.1
Nettleton, D.2
McCarthy, D.3
Smyth, G.4
-
13
-
-
50649089207
-
RNA-seq: an assessment of technical reproducability and comparison with gene expression arrays.
-
Marioni JC, Mason C, Mane SM, Stephens S, Gilad Y. 2008. RNA-seq: an assessment of technical reproducability and comparison with gene expression arrays. Genome Research 18:1509-1517 DOI 10.1101/gr.079558.108.
-
(2008)
Genome Research
, vol.18
, pp. 1509-1517
-
-
Marioni, J.C.1
Mason, C.2
Mane, S.M.3
Stephens, S.4
Gilad, Y.5
-
14
-
-
46249106990
-
Mapping and quantifying mammilian transcriptomes by RNA-seq
-
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammilian transcriptomes by RNA-seq. Nature Methods 5(7):621-628 DOI 10.1038/nmeth.1226.
-
(2008)
Nature Methods
, vol.5
, Issue.7
, pp. 621-628
-
-
Mortazavi, A.1
Williams, B.A.2
McCue, K.3
Schaeffer, L.4
Wold, B.5
-
15
-
-
33748651016
-
Estimating the number of true null hypotheses from a histogram of values
-
Nettleton D, Hwang J, Caldo R, Wose R. 2006. Estimating the number of true null hypotheses from a histogram of values. Journal of Agricultural, Biological and Environmental Statistics 11(3):337-356 DOI 10.1198/108571106X129135.
-
(2006)
Journal of Agricultural, Biological and Environmental Statistics
, vol.11
, Issue.3
, pp. 337-356
-
-
Nettleton, D.1
Hwang, J.2
Caldo, R.3
Wose, R.4
-
16
-
-
77950460661
-
Understanding mechanisms underlying human gene expression variation with RNA sequencing.
-
Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras J-B, Stephens M, Gilad Y, Pritchard JK. 2010. Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464:768-772 DOI 10.1038/nature08872.
-
(2010)
Nature
, vol.464
, pp. 768-772
-
-
Pickrell, J.K.1
Marioni, J.C.2
Pai, A.A.3
Degner, J.F.4
Engelhardt, B.E.5
Nkadori, E.6
Veyrieras, J.-B.7
Stephens, M.8
Gilad, Y.9
Pritchard, J.K.10
-
18
-
-
84907687412
-
edgeR: differential expression analysis of digital expression data user's guide.
-
Robinson M, McCarthy D, Chen Y, Smyth G. 2013. edgeR: differential expression analysis of digital expression data user's guide. Available at http://www.bioconductor.org/packages/release/bioc/vignettes/edger/inst/doc/edgerusersguide.pdf
-
(2013)
-
-
Robinson, M.1
McCarthy, D.2
Chen, Y.3
Smyth, G.4
-
19
-
-
75249087100
-
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
-
Robinson M, McCarthy D, Smyth G. 2010. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26:139-140 DOI 10.1093/bioinformatics/btp616.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.1
McCarthy, D.2
Smyth, G.3
-
20
-
-
77953176036
-
A scaling normalization method for differential expression analysis of RNA-seq data.
-
Robinson MD, Oshlack A. 2010. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biology 11:R25 DOI 10.1186/gb-2010-11-3-r25.
-
(2010)
Genome Biology
, vol.11
, pp. R25
-
-
Robinson, M.D.1
Oshlack, A.2
-
21
-
-
36448981743
-
Moderated statistical tests for assessing differences in tag abundance
-
Robinson M, Smyth G. 2007. Moderated statistical tests for assessing differences in tag abundance. Bioinformatics 23(21):2881-2887 DOI 10.1093/bioinformatics/btm453.
-
(2007)
Bioinformatics
, vol.23
, Issue.21
, pp. 2881-2887
-
-
Robinson, M.1
Smyth, G.2
-
22
-
-
41149085992
-
Small-sample estimation of negative binomial dispersion, with applications to SAGE data
-
Robinson M, Smyth G. 2008. Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics 9(2):321-332 DOI 10.1093/biostatistics/kxm030.
-
(2008)
Biostatistics
, vol.9
, Issue.2
, pp. 321-332
-
-
Robinson, M.1
Smyth, G.2
-
23
-
-
84866158885
-
Efficient experimental design and analysis strategies for the detection of differential expression using rna-sequencing.
-
Robles J, Qureshi S, Stephen S, Wilson S, Burden C, Taylor J. 2012. Efficient experimental design and analysis strategies for the detection of differential expression using rna-sequencing. BMC Genomics 13:484 DOI 10.1186/1471-2164-13-484.
-
(2012)
BMC Genomics
, vol.13
, pp. 484
-
-
Robles, J.1
Qureshi, S.2
Stephen, S.3
Wilson, S.4
Burden, C.5
Taylor, J.6
-
24
-
-
4544341015
-
Linear models and empirical bayes methods for assessing differential expression in microarray experiments.
-
Smyth G. 2004. Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology 3:Article 3 DOI 10.2202/1544-6115.1027.
-
(2004)
Statistical Applications in Genetics and Molecular Biology
, vol.3
-
-
Smyth, G.1
-
25
-
-
84874677498
-
A comparison of methods for differential expression analysis of RNA-seq data.
-
Soneson C, Delorenzi M. 2013. A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics 14:91 DOI 10.1186/1471-2105-14-91.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 91
-
-
Soneson, C.1
Delorenzi, M.2
-
26
-
-
85015829733
-
Biokanga: a suite of high performance bioinformatics applications.
-
Stephen S, Cullerne D, Spriggs A, Helliwell C, Lovell D, Taylor J. 2012. Biokanga: a suite of high performance bioinformatics applications. Available at http://code.google.com/p/biokanga/.
-
(2012)
-
-
Stephen, S.1
Cullerne, D.2
Spriggs, A.3
Helliwell, C.4
Lovell, D.5
Taylor, J.6
-
28
-
-
0032394989
-
Nonlinear regression, quasi likelihood, and overdispersion in generalised linear models.
-
Tjur T. 1998. Nonlinear regression, quasi likelihood, and overdispersion in generalised linear models. American Statistician 52:222-227.
-
(1998)
American Statistician
, vol.52
, pp. 222-227
-
-
Tjur, T.1
|