-
1
-
-
84861414639
-
Comprehensive literature review and statistical considerations for microarray meta-analysis
-
Tseng GC, Ghosh D, Feingold E, Comprehensive literature review and statistical considerations for microarray meta-analysis, Nucl Acids Res 40(9):3785-3799, 2012
-
(2012)
Nucl Acids Res
, vol.40
, Issue.9
, pp. 3785-3799
-
-
Tseng, G.C.1
Ghosh, D.2
Feingold, E.3
-
4
-
-
80054716507
-
Software and tools for microarray data analysis
-
Mehta JP, Rani S, Software and tools for microarray data analysis, Methods Mol Biol 784:41-53, 2011
-
(2011)
Methods Mol Biol
, vol.784
, pp. 41-53
-
-
Mehta, J.P.1
Rani, S.2
-
5
-
-
0037311919
-
TM4: A free open-source system for microarray data management and analysis
-
Saeed AI, Sharov V, White J, Li J, Liang W, Bhagabati N, Braisted J, Klapa M, Currier T, Thiagarajan M, Sturn A, Snuffin M, Rezantsev A, Popov D, Ryltsov A, Kostukovich E, Borisovsky I, Liu Z, Vinsavich A, Trush V, Quackenbush J, TM4: A free, open-source system for microarray data management and analysis, Biotechniques 34(2):374-378, 2003
-
(2003)
Biotechniques
, vol.34
, Issue.2
, pp. 374-378
-
-
Saeed, A.I.1
Sharov, V.2
White, J.3
Li, J.4
Liang, W.5
Bhagabati, N.6
Braisted, J.7
Klapa, M.8
Currier, T.9
Thiagarajan, M.10
Sturn, A.11
Snuffin, M.12
Rezantsev, A.13
Popov, D.14
Ryltsov, A.15
Kostukovich, E.16
Borisovsky, I.17
Liu, Z.18
Vinsavich, A.19
Trush, V.20
Quackenbush, J.21
more..
-
6
-
-
0035942271
-
Significance analysis of microarrays applied to the ionizing radiation response
-
Tusher VG, Tibshirani R, Chu G, Significance analysis of microarrays applied to the ionizing radiation response, Proc Natl Acad Sci U S A 98(9):5116-5121, 2001
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, Issue.9
, pp. 5116-5121
-
-
Tusher, V.G.1
Tibshirani, R.2
Chu, G.3
-
7
-
-
19544391863
-
A web-based tool for principal component and signi ficance analysis of microarray data
-
Sharov AA, Dudekula DB, Ko MS, A web-based tool for principal component and signi ficance analysis of microarray data, Bioinformatics 21(10):2548-2549, 2005
-
(2005)
Bioinformatics
, vol.21
, Issue.10
, pp. 2548-2549
-
-
Sharov, A.A.1
Dudekula, D.B.2
Ko, M.S.3
-
8
-
-
0036578644
-
GenMAPP a new tool for viewing and analyzing microarray data on biological pathways
-
Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR, GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways, Nat Genet 31(1):19-20, 2002
-
(2002)
Nat Genet
, vol.31
, Issue.1
, pp. 19-20
-
-
Dahlquist, K.D.1
Salomonis, N.2
Vranizan, K.3
Lawlor, S.C.4
Conklin, B.R.5
-
9
-
-
0037263812
-
MAPPFinder: Using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data
-
Doniger SW, Salomonis N, Dahlquist KD, Vranizan K, Lawlor SC, Conklin BR, MAPPFinder: Using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data, Genome Biol 4(1):R7, 2003
-
(2003)
Genome Biol
, vol.4
, Issue.1
, pp. R7
-
-
Doniger, S.W.1
Salomonis, N.2
Dahlquist, K.D.3
Vranizan, K.4
Lawlor, S.C.5
Conklin, B.R.6
-
10
-
-
24644470505
-
Ontological analysis of gene expression data: Current tools limitations, and open problems
-
Khatri P, Draghici S, Ontological analysis of gene expression data: current tools, limitations, and open problems, Bioinformatics 21(18):3587-3595, 2005
-
(2005)
Bioinformatics
, vol.21
, Issue.18
, pp. 3587-3595
-
-
Khatri, P.1
Draghici, S.2
-
11
-
-
34547571929
-
Onto-Tools: New additions and improvements in 2006
-
Web Server issue
-
Khatri P, Voichita C, Kattan K, Ansari N, Khatri A, Georgescu C, Tarca AL, Draghici S, Onto-Tools: New additions and improvements in 2006, Nucl Acids Res 35 (Web Server issue):W206-W211, 2007
-
(2007)
Nucl Acids Res
, vol.35
, pp. W206-W211
-
-
Khatri, P.1
Voichita, C.2
Kattan, K.3
Ansari, N.4
Khatri, A.5
Georgescu, C.6
Tarca, A.L.7
Draghici, S.8
-
12
-
-
58549112996
-
Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists
-
Huang da W, Sherman BT, Lempicki RA, Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists, Nucl Acids Res 37(1):1-13, 2009
-
(2009)
Nucl Acids Res
, vol.37
, Issue.1
, pp. 1-13
-
-
Huang Da, W.1
Sherman, B.T.2
Lempicki, R.A.3
-
13
-
-
27344435774
-
Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles
-
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP, Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles, Proc Natl Acad Sci U S A 102(43):15545-15550, 2005
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, Issue.43
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Ma, G.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
Mesirov, J.P.11
-
14
-
-
84955237698
-
-
Available at
-
Gentleman R, Ruschhaupt M, Huber W, Lusa L, Meta-analysis for microarray experiments, Available at http://www.bioconductor.org/packages/release/bioc/vignettes/GeneMeta/inst/doc/GeneMeta.pdf, 2014
-
(2014)
Meta-analysis for Microarray Experiments
-
-
Gentleman, R.1
Ruschhaupt, M.2
Huber, W.3
Lusa, L.4
-
15
-
-
39549116496
-
A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments
-
Choi H, Shen R, Chinnaiyan AM, Ghosh D, A latent variable approach for meta-analysis of gene expression data from multiple microarray experiments, BMC Bioinformatics 8:364, 2007
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 364
-
-
Choi, H.1
Shen, R.2
Chinnaiyan, A.M.3
Ghosh, D.4
-
16
-
-
33846904113
-
An Introduction to MAMA (Meta-Analysis of MicroArray data) System
-
Zhang Z, Fenstermacher D, An Introduction to MAMA (Meta-Analysis of MicroArray data) System, Conf Proc IEEE Eng Med Biol Soc, Vol. 7, pp. 7730-7733, 2005
-
(2005)
Conf Proc IEEE Eng Med Biol Soc
, vol.7
, pp. 7730-7733
-
-
Zhang, Z.1
Fenstermacher, D.2
-
17
-
-
78651339534
-
NCBI GEO: Archive for functional genomics data sets 10 years on
-
Database issue
-
Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A, NCBI GEO: Archive for functional genomics data sets 10 years on, Nucl Acids Res 39(Database issue):D1005-D1010, 2011
-
(2011)
Nucl Acids Res
, vol.39
, pp. D1005-D1010
-
-
Barrett, T.1
Troup, D.B.2
Wilhite, S.E.3
Ledoux, P.4
Evangelista, C.5
Kim, I.F.6
Tomashevsky, M.7
Marshall, K.A.8
Phillippy, K.H.9
Sherman, P.M.10
Muertter, R.N.11
Holko, M.12
Ayanbule, O.13
Yefanov, A.14
Soboleva, A.15
-
18
-
-
84941103248
-
ArrayExpress update-simplifying data submissions
-
Database issue
-
Kolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T, Megy K, Pilicheva E, Rustici G, Tikhonov A, Parkinson H, Petryszak R, Sarkans U, Brazma A, ArrayExpress update-simplifying data submissions, Nucl Acids Res 43(Database issue):D1113-D1116, 2014
-
(2014)
Nucl Acids Res
, vol.43
, pp. D1113-D1116
-
-
Kolesnikov, N.1
Hastings, E.2
Keays, M.3
Melnichuk, O.4
Tang, Y.A.5
Williams, E.6
Dylag, M.7
Kurbatova, N.8
Brandizi, M.9
Burdett, T.10
Megy, K.11
Pilicheva, E.12
Rustici, G.13
Tikhonov, A.14
Parkinson, H.15
Petryszak, R.16
Sarkans, U.17
Brazma, A.18
-
19
-
-
48449092932
-
Microarray retriever: A web-based tool for searching and large scale retrieval of public microarray data
-
Web Server issue
-
Ivliev AE, 't Hoen PA, Villerius MP, den Dunnen JT, Brandt BW, Microarray retriever: A web-based tool for searching and large scale retrieval of public microarray data, Nucl Acids Res 36(Web Server issue):W327-W331, 2008
-
(2008)
Nucl Acids Res
, vol.36
, pp. W327-W331
-
-
Ivliev, A.E.1
Hoen, P.A.T.2
Villerius, M.P.3
Den Dunnen, J.T.4
Brandt, B.W.5
-
20
-
-
84859736980
-
Generation of mouse ES cell lines engineered for the forced induction of transcription factors
-
Correa-Cerro LS, Piao Y, Sharov AA, Nishiyama A, Cadet JS, Yu H, Sharova LV, Xin L, Hoang HG, Thomas M, Qian Y, Dudekula DB, Meyers E, Binder BY, Mowrer G, Bassey U, Longo DL, Schlessinger D, Ko MSH, Generation of mouse ES cell lines engineered for the forced induction of transcription factors, Sci Rep 1:176, 2011
-
(2011)
Sci Rep
, vol.1
, pp. 176
-
-
Correa-Cerro, L.S.1
Piao, Y.2
Sharov, A.A.3
Nishiyama, A.4
Cadet, J.S.5
Yu, H.6
Sharova, L.V.7
Xin, L.8
Hoang, H.G.9
Thomas, M.10
Qian, Y.11
Dudekula, D.B.12
Meyers, E.13
Binder, B.Y.14
Mowrer, G.15
Bassey, U.16
Longo, D.L.17
Schlessinger, D.18
Ko, M.S.H.19
-
21
-
-
0037007048
-
Large-scale analysis of the human and mouse transcriptomes
-
Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, Orth AP, Vega RG, Sapinoso LM, Moqrich A, Patapoutian A, Hampton GM, Schultz PG, Hogenesch JB, Large-scale analysis of the human and mouse transcriptomes, Proc Natl Acad Sci U S A 99(7):4465-4470, 2002
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, Issue.7
, pp. 4465-4470
-
-
Su, A.I.1
Cooke, M.P.2
Ching, K.A.3
Hakak, Y.4
Walker, J.R.5
Wiltshire, T.6
Orth, A.P.7
Vega, R.G.8
Sapinoso, L.M.9
Moqrich, A.10
Patapoutian, A.11
Hampton, G.M.12
Schultz, P.G.13
Hogenesch, J.B.14
-
22
-
-
76249090489
-
BioGPS: An extensible and customizable portal for querying and organizing gene annotation resources
-
Wu C, Orozco C, Boyer J, Leglise M, Goodale J, Batalov S, Hodge CL, Haase J, Janes J, Huss JW 3rd, Su AI, BioGPS: An extensible and customizable portal for querying and organizing gene annotation resources, Genome Biol 10(11):R130, 2009
-
(2009)
Genome Biol
, vol.10
, Issue.11
, pp. R130
-
-
Wu, C.1
Orozco, C.2
Boyer, J.3
Leglise, M.4
Goodale, J.5
Batalov, S.6
Hodge, C.L.7
Haase, J.8
Janes, J.9
Huss, J.W.10
Su, A.I.11
-
23
-
-
84900303453
-
Transcriptional landscape of the prenatal human brain
-
Miller JA, Ding SL, Sunkin SM, Smith KA, Ng L, Szafer A, Ebbert A, Riley ZL, Royall JJ, Aiona K, Arnold JM, Bennet C, Bertagnolli D, Brouner K, Butler S, Caldejon S, Carey A, Cuhaciyan C, Dalley RA, Dee N, Dolbeare TA, Facer BA, Feng D, Fliss TP, Gee G, Goldy J, Gourley L, Gregor BW, Gu G, Howard RE, Jochim JM, Kuan CL, Lau C, Lee CK, Lee F, Lemon TA, Lesnar P, McMurray B, Mastan N, Mosqueda N, Naluai-Cecchini T, Ngo NK, Nyhus J, Oldre A, Olson E, Parente J, Parker PD, Parry SE, Stevens A, Pletikos M, Reding M, Roll K, Sandman D, Sarreal M, Shapouri S, Shapovalova NV, Shen EH, Sjoquist N, Slaughterbeck CR, Smith M, Sodt AJ, Williams D, Zollei L, Fischl B, Gerstein MB, Geschwind DH, Glass IA, Hawrylycz MJ, Hevner RF, Huang H, Jones AR, Knowles JA, Levitt P, Phillips JW, Sestan N, Wohnoutka P, Dang C, Bernard A, Hohmann JG, Lein ES, Transcriptional landscape of the prenatal human brain, Nature 508(7495):199-206, 2014
-
(2014)
Nature
, vol.508
, Issue.7495
, pp. 199-206
-
-
Miller, J.A.1
Ding, S.L.2
Sunkin, S.M.3
Smith, K.A.4
Ng, L.5
Szafer, A.6
Ebbert, A.7
Riley, Z.L.8
Royall, J.J.9
Aiona, K.10
Arnold, J.M.11
Bennet, C.12
Bertagnolli, D.13
Brouner, K.14
Butler, S.15
Caldejon, S.16
Carey, A.17
Cuhaciyan, C.18
Dalley, R.A.19
Dee, N.20
Dolbeare, T.A.21
Facer, B.A.22
Feng, D.23
Fliss, T.P.24
Gee, G.25
Goldy, J.26
Gourley, L.27
Gregor, B.W.28
Gu, G.29
Howard, R.E.30
Jochim, J.M.31
Kuan, C.L.32
Lau, C.33
Lee, C.K.34
Lee, F.35
Lemon, T.A.36
Lesnar, P.37
McMurray, B.38
Mastan, N.39
Mosqueda, N.40
Naluai-Cecchini, T.41
Ngo, N.K.42
Nyhus, J.43
Oldre, A.44
Olson, E.45
Parente, J.46
Parker, P.D.47
Parry, S.E.48
Stevens, A.49
Pletikos, M.50
Reding, M.51
Roll, K.52
Sandman, D.53
Sarreal, M.54
Shapouri, S.55
Shapovalova, N.V.56
Shen, E.H.57
Sjoquist, N.58
Slaughterbeck, C.R.59
Smith, M.60
Sodt, A.J.61
Williams, D.62
Zollei, L.63
Fischl, B.64
Gerstein, M.B.65
Geschwind, D.H.66
Glass, I.A.67
Hawrylycz, M.J.68
Hevner, R.F.69
Huang, H.70
Jones, A.R.71
Knowles, J.A.72
Levitt, P.73
Phillips, J.W.74
Sestan, N.75
Wohnoutka, P.76
Dang, C.77
Bernard, A.78
Hohmann, J.G.79
Lein, E.S.80
more..
-
24
-
-
84862192725
-
The UniProt-GO Annotation database in 2011
-
Database issue
-
Dimmer EC, Huntley RP, Alam-Faruque Y, Sawford T, O'Donovan C, Martin MJ, Bely B, Browne P, Mun Chan W, Eberhardt R, Gardner M, Laiho K, Legge D, Magrane M, Pichler K, Poggioli D, Sehra H, Auchincloss A, Axelsen K, Blatter MC, Boutet E, Braconi-Quintaje S, Breuza L, Bridge A, Coudert E, Estreicher A, Famiglietti L, Ferro-Rojas S, Feuermann M, Gos A, Gruaz-Gumowski N, Hinz U, Hulo C, James J, Jimenez S, Jungo F, Keller G, Lemercier P, Lieberherr D, Masson P, Moinat M, Pedruzzi I, Poux S, Rivoire C, Roechert B, Schneider M, Stutz A, Sundaram S, Tognolli M, Bougueleret L, Argoud-Puy G, Cusin I, Duek-Roggli P, Xenarios I, Apweiler R, The UniProt-GO Annotation database in 2011, Nucl Acids Res 40(Database issue):D565-D570, 2011
-
(2011)
Nucl Acids Res
, vol.40
, pp. D565-D570
-
-
Dimmer, E.C.1
Huntley, R.P.2
Alam-Faruque, Y.3
Sawford, T.4
O'Donovan, C.5
Martin, M.J.6
Bely, B.7
Browne, P.8
Mun Chan, W.9
Eberhardt, R.10
Gardner, M.11
Laiho, K.12
Legge, D.13
Magrane, M.14
Pichler, K.15
Poggioli, D.16
Sehra, H.17
Auchincloss, A.18
Axelsen, K.19
Blatter, M.C.20
Boutet, E.21
Braconi-Quintaje, S.22
Breuza, L.23
Bridge, A.24
Coudert, E.25
Estreicher, A.26
Famiglietti, L.27
Ferro-Rojas, S.28
Feuermann, M.29
Gos, A.30
Gruaz-Gumowski, N.31
Hinz, U.32
Hulo, C.33
James, J.34
Jimenez, S.35
Jungo, F.36
Keller, G.37
Lemercier, P.38
Lieberherr, D.39
Masson, P.40
Moinat, M.41
Pedruzzi, I.42
Poux, S.43
Rivoire, C.44
Roechert, B.45
Schneider, M.46
Stutz, A.47
Sundaram, S.48
Tognolli, M.49
Bougueleret, L.50
Argoud-Puy, G.51
Cusin, I.52
Duek-Roggli, P.53
Xenarios, I.54
Apweiler, R.55
more..
-
25
-
-
84891760956
-
Data, information, knowledge and principle: Back to metabolism in KEGG
-
Database issue
-
Kanehisa M, Goto S, Sato Y, Kawashima M, Furumichi M, Tanabe M, Data, information, knowledge and principle: Back to metabolism in KEGG, Nucl Acids Res 42(Database issue):D199-D205, 2013
-
(2013)
Nucl Acids Res
, vol.42
, pp. D199-D205
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Kawashima, M.4
Furumichi, M.5
Tanabe, M.6
-
26
-
-
77149125896
-
Systematic analysis comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information
-
Zhang Y, De S, Garner JR, Smith K, Wang SA, Becker KG, Systematic analysis, comparison, and integration of disease based human genetic association data and mouse genetic phenotypic information, BMC Med Genomics 3:1, 2010
-
(2010)
BMC Med Genomics
, vol.3
, pp. 1
-
-
Zhang, Y.1
De S Garner, J.R.2
Smith, K.3
Wang, S.A.4
Becker, K.G.5
-
27
-
-
84865739425
-
Architecture of the human regulatory network derived from ENCODE data
-
Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M, Architecture of the human regulatory network derived from ENCODE data, Nature 489(7414):91-100, 2012
-
(2012)
Nature
, vol.489
, Issue.7414
, pp. 91-100
-
-
Gerstein, M.B.1
Kundaje, A.2
Hariharan, M.3
Landt, S.G.4
Yan, K.K.5
Cheng, C.6
Mu, X.J.7
Khurana, E.8
Rozowsky, J.9
Alexander, R.10
Min, R.11
Alves, P.12
Abyzov, A.13
Addleman, N.14
Bhardwaj, N.15
Boyle, A.P.16
Cayting, P.17
Charos, A.18
Chen, D.Z.19
Cheng, Y.20
Clarke, D.21
Eastman, C.22
Euskirchen, G.23
Frietze, S.24
Fu, Y.25
Gertz, J.26
Grubert, F.27
Harmanci, A.28
Jain, P.29
Kasowski, M.30
Lacroute, P.31
Leng, J.32
Lian, J.33
Monahan, H.34
O'Geen, H.35
Ouyang, Z.36
Partridge, E.C.37
Patacsil, D.38
Pauli, F.39
Raha, D.40
Ramirez, L.41
Reddy, T.E.42
Reed, B.43
Shi, M.44
Slifer, T.45
Wang, J.46
Wu, L.47
Yang, X.48
Yip, K.Y.49
Zilberman-Schapira, G.50
Batzoglou, S.51
Sidow, A.52
Farnham, P.J.53
Myers, R.M.54
Weissman, S.M.55
Snyder, M.56
more..
-
28
-
-
84941145210
-
The BioGRID interaction database 2015 update
-
Database issue
-
Chatr-Aryamontri A, Breitkreutz BJ, Oughtred R, Boucher L, Heinicke S, Chen D, Stark C, Breitkreutz A, Kolas N, O'Donnell L, Reguly T, Nixon J, Ramage L, Winter A, Sellam A, Chang C, Hirschman J, Theesfeld C, Rust J, Livstone MS, Dolinski K, Tyers M, The BioGRID interaction database: 2015 update, Nucl Acids Res 43(Database issue):D470-D478, 2014
-
(2014)
Nucl Acids Res
, vol.43
, pp. D470-D478
-
-
Chatr-Aryamontri, A.1
Breitkreutz, B.J.2
Oughtred, R.3
Boucher, L.4
Heinicke, S.5
Chen, D.6
Stark, C.7
Breitkreutz, A.8
Kolas, N.9
O'Donnell, L.10
Reguly, T.11
Nixon, J.12
Ramage, L.13
Winter, A.14
Sellam, A.15
Chang, C.16
Hirschman, J.17
Theesfeld, C.18
Rust, J.19
Livstone, M.S.20
Dolinski, K.21
Tyers, M.22
more..
-
29
-
-
0037316303
-
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
-
Bolstad BM, Irizarry RA, Astrand M, Speed TP, A comparison of normalization methods for high density oligonucleotide array data based on variance and bias, Bioinformatics 19 (2):185-193, 2003
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 185-193
-
-
Bolstad, B.M.1
Irizarry, R.A.2
Astrand, M.3
Speed, T.P.4
-
30
-
-
84859885816
-
Di®erential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cu®links
-
Trapnell C, Roberts A, Go® L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L, Di®erential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cu®links, Nat Protoc 7(3):562-578, 2012
-
(2012)
Nat Protoc
, vol.7
, Issue.3
, pp. 562-578
-
-
Trapnell, C.1
Roberts, A.2
Go, L.3
Pertea, G.4
Kim, D.5
Kelley, D.R.6
Pimentel, H.7
Salzberg, S.L.8
Rinn, J.L.9
Pachter, L.10
-
31
-
-
0001677717
-
Controlling the false discovery rate A practical and powerful approach to multiple testing
-
Benjamini Y, Hochberg Y, Controlling the false discovery rate A practical and powerful approach to multiple testing, J R Stat Soc B 57:289-300, 1995
-
(1995)
J R Stat Soc B
, vol.57
, pp. 289-300
-
-
Benjamini, Y.1
Hochberg, Y.2
-
32
-
-
84955324114
-
Use of the half-normal probability plot to identify significant e®ects for microarray data 2002
-
New York, NY
-
Dyson G, Wu J, Use of the half-normal probability plot to identify significant e®ects for microarray data, 2002 Joint Statistical Meeting (JSM), New York, NY, 2002
-
(2002)
Joint Statistical Meeting (JSM)
-
-
Dyson, G.1
Wu, J.2
-
34
-
-
0000326805
-
Selected quantitative techniques
-
in Lindzey G (ed.) Addison Wesley, Cambridge, MA
-
Mosteller F, Bush RR, Selected quantitative techniques, in Lindzey G (ed.), Handbook of Social Psychology, Vol. 1, pp. 289-334, Addison Wesley, Cambridge, MA, 1954
-
(1954)
Handbook of Social Psychology
, vol.1
, pp. 289-334
-
-
Mosteller, F.1
Bush, R.R.2
-
35
-
-
0022992740
-
Meta-analysis in clinical trials
-
DerSimonian R, Laird N, Meta-analysis in clinical trials, Control Clin Trials 7(3):177-188, 1986
-
(1986)
Control Clin Trials
, vol.7
, Issue.3
, pp. 177-188
-
-
DerSimonian, R.1
Laird, N.2
-
36
-
-
0035162272
-
Database resources of the National Center for Biotechnology Information
-
Wheeler DL, Church DM, Lash AE, Leipe DD, Madden TL, Pontius JU, Schuler GD, Schriml LM, Tatusova TA, Wagner L, Rapp BA, Database resources of the National Center for Biotechnology Information, Nucl Acids Res 29(1):11-16, 2001
-
(2001)
Nucl Acids Res
, vol.29
, Issue.1
, pp. 11-16
-
-
Wheeler, D.L.1
Church, D.M.2
Lash, A.E.3
Leipe, D.D.4
Madden, T.L.5
Pontius, J.U.6
Schuler, G.D.7
Schriml, L.M.8
Tatusova, T.A.9
Wagner, L.10
Rapp, B.A.11
-
37
-
-
25444502609
-
PAGE: Parametric analysis of gene set enrichment
-
Kim SY, Volsky DJ, PAGE: Parametric analysis of gene set enrichment, BMC Bioinformatics 6:144, 2005
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 144
-
-
Kim, S.Y.1
Volsky, D.J.2
-
38
-
-
84905259973
-
Chromatin properties of regulatory DNA probed by manipulation of transcription factors
-
Sharov AA, Nishiyama A, Qian Y, Dudekula DB, Longo DL, Schlessinger D, Ko MS, Chromatin properties of regulatory DNA probed by manipulation of transcription factors, J Comput Biol 21(8):569-577, 2014
-
(2014)
J Comput Biol
, vol.21
, Issue.8
, pp. 569-577
-
-
Sharov, A.A.1
Nishiyama, A.2
Qian, Y.3
Dudekula, D.B.4
Longo, D.L.5
Schlessinger, D.6
Ko, M.S.7
|