-
1
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, et al.Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009; 326:289-93. doi: 10.1126/science.1181369.
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
van Berkum, N.L.2
Williams, L.3
Imakaev, M.4
Ragoczy, T.5
Telling, A.6
-
2
-
-
84878011578
-
Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
-
Dekker J, Marti-Renom MA, Mirny LA. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat Rev Genet. 2013; 14:390-403. doi: 10.1038/nrg3454.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 390-403
-
-
Dekker, J.1
Marti-Renom, M.A.2
Mirny, L.A.3
-
3
-
-
84861095603
-
Topological domains in mammalian genomes identified by analysis of chromatin interactions
-
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, et al.Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012; 485:376-80. doi: 10.1038/nature11082.
-
(2012)
Nature
, vol.485
, pp. 376-380
-
-
Dixon, J.R.1
Selvaraj, S.2
Yue, F.3
Kim, A.4
Li, Y.5
Shen, Y.6
-
4
-
-
84887620842
-
A high-resolution map of the three-dimensional chromatin interactome in human cells
-
Jin F, Li Y, Dixon JR, Selvaraj S, Ye Z, Lee AY, et al.A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature. 2013; 503:290-4. doi: 10.1038/nature12644.
-
(2013)
Nature
, vol.503
, pp. 290-294
-
-
Jin, F.1
Li, Y.2
Dixon, J.R.3
Selvaraj, S.4
Ye, Z.5
Lee, A.Y.6
-
5
-
-
84888018217
-
Organization of the mitotic chromosome
-
Naumova N, Imakaev M, Fudenberg G, Zhan Y, Lajoie BR, Mirny LA, et al.Organization of the mitotic chromosome. Science. 2013; 342:948-53. doi: 10.1126/science.1236083.
-
(2013)
Science
, vol.342
, pp. 948-953
-
-
Naumova, N.1
Imakaev, M.2
Fudenberg, G.3
Zhan, Y.4
Lajoie, B.R.5
-
6
-
-
84911478490
-
Topologically associating domains are stable units of replication-timing regulation
-
Pope BD, Ryba T, Dileep V, Yue F, Wu W, Denas O, et al.Topologically associating domains are stable units of replication-timing regulation. Nature. 2014; 515:402-5. doi: 10.1038/nature13986.
-
(2014)
Nature
, vol.515
, pp. 402-405
-
-
Pope, B.D.1
Ryba, T.2
Dileep, V.3
Yue, F.4
Wu, W.5
Denas, O.6
-
7
-
-
84919949716
-
A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping
-
Rao SSP, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, et al.A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014; 159:1665-80. doi: 10.1016/j.cell.2014.11.021.
-
(2014)
Cell
, vol.159
, pp. 1665-1680
-
-
Rao, S.S.P.1
Huntley, M.H.2
Durand, N.C.3
Stamenova, E.K.4
Bochkov, I.D.5
Robinson, J.T.6
-
8
-
-
84923366733
-
Chromatin architecture reorganization during stem cell differentiation
-
Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, et al.Chromatin architecture reorganization during stem cell differentiation. Nature. 2015; 518:331-6. doi: 10.1038/nature14222.
-
(2015)
Nature
, vol.518
, pp. 331-336
-
-
Dixon, J.R.1
Jung, I.2
Selvaraj, S.3
Shen, Y.4
Antosiewicz-Bourget, J.E.5
-
9
-
-
80053304450
-
High density DNA methylation array with single CpG site resolution,
-
Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, et al.High density DNA methylation array with single CpG site resolution,. Genomics. 2011; 98:288-95. doi: 10.1016/j.ygeno.2011.07.007.
-
(2011)
Genomics
, vol.98
, pp. 288-295
-
-
Bibikova, M.1
Barnes, B.2
Tsan, C.3
Ho, V.4
Klotzle, B.5
Le, J.M.6
-
10
-
-
30044449116
-
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)
-
Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, et al.Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res. 2006; 16:123-31. doi: 10.1101/gr.4074106.
-
(2006)
Genome Res
, vol.16
, pp. 123-131
-
-
Crawford, G.E.1
Holt, I.E.2
Whittle, J.3
Webb, B.D.4
Tai, D.5
Davis, S.6
-
11
-
-
38649099445
-
High-resolution mapping and characterization of open chromatin across the genome
-
Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, et al.High-resolution mapping and characterization of open chromatin across the genome. Cell. 2008; 132:311-22. doi: 10.1016/j.cell.2007.12.014.
-
(2008)
Cell
, vol.132
, pp. 311-322
-
-
Boyle, A.P.1
Davis, S.2
Shulha, H.P.3
Meltzer, P.4
Margulies, E.H.5
Weng, Z.6
-
12
-
-
84905405443
-
Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity
-
Smallwood SA, Lee HJ, Angermueller C, Krueger F, Saadeh H, Peat J, et al.Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity. Nat Methods. 2014; 11:817-20. doi: 10.1038/nmeth.3035.
-
(2014)
Nat Methods
, vol.11
, pp. 817-820
-
-
Smallwood, S.A.1
Lee, H.J.2
Angermueller, C.3
Krueger, F.4
Saadeh, H.5
-
13
-
-
84930006926
-
Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing
-
Cusanovich DA, Daza R, Adey A, Pliner HA, Christiansen L, Gunderson KL, et al.Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing. Science. 2015; 348:910-14. doi: 10.1126/science.aab1601.
-
(2015)
Science
, vol.348
, pp. 910-914
-
-
Cusanovich, D.A.1
Daza, R.2
Adey, A.3
Pliner, H.A.4
Christiansen, L.5
Gunderson, K.L.6
-
14
-
-
84864819611
-
The Cancer Genome Atlas
-
TCGA. The Cancer Genome Atlas. http://cancergenome.nih.gov.
-
-
-
-
15
-
-
84866997011
-
Iterative correction of Hi-C data reveals hallmarks of chromosome organization
-
Imakaev M, Fudenberg G, McCord RP, Naumova N, Goloborodko A, Lajoie BR, et al.Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat Methods. 2012; 9:999-1003. doi: 10.1038/nmeth.2148.
-
(2012)
Nat Methods
, vol.9
, pp. 999-1003
-
-
Imakaev, M.1
Fudenberg, G.2
McCord, R.P.3
Naumova, N.4
Goloborodko, A.5
Lajoie, B.R.6
-
16
-
-
0025884418
-
The distribution of genes in the human genome
-
Mouchiroud D, D'Onofrio G, Aïssani B, Macaya G, Gautier C, Bernardi G. The distribution of genes in the human genome. Gene. 1991; 100:181-7.
-
(1991)
Gene
, vol.100
, pp. 181-187
-
-
Mouchiroud, D.1
D'Onofrio, G.2
Aïssani, B.3
Macaya, G.4
Gautier, C.5
Bernardi, G.6
-
17
-
-
84883703352
-
DNA methylation contributes to natural human variation
-
Heyn H, Moran S, Hernando-Herraez I, Sayols S, Gomez A, Sandoval J, et al.DNA methylation contributes to natural human variation. Genome Res. 2013; 23:1363-72. doi: 10.1101/gr.154187.112.
-
(2013)
Genome Res
, vol.23
, pp. 1363-1372
-
-
Heyn, H.1
Moran, S.2
Hernando-Herraez, I.3
Sayols, S.4
Gomez, A.5
-
18
-
-
79956330964
-
CpG islands and the regulation of transcription
-
Deaton AM, Bird A. CpG islands and the regulation of transcription. Genes Dev. 2011; 25:1010-22. doi: 10.1101/gad.2037511.
-
(2011)
Genes Dev
, vol.25
, pp. 1010-1022
-
-
Deaton, A.M.1
Bird, A.2
-
19
-
-
84897489039
-
The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts
-
Wagner JR, Busche S, Ge B, Kwan T, Pastinen T, Blanchette M. The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts. Genome Biol. 2014; 15:37. doi: 10.1093/bioinformatics/bth088.
-
(2014)
Genome Biol
, vol.15
, pp. 37
-
-
Wagner, J.R.1
Busche, S.2
Ge, B.3
Kwan, T.4
Pastinen, T.5
Blanchette, M.6
-
20
-
-
70450217879
-
Human DNA methylomes at base resolution show widespread epigenomic differences
-
Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon GC, Tonti-Filippini J, et al.Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009; 462:315-22. doi: 10.1038/nature08514.
-
(2009)
Nature
, vol.462
, pp. 315-322
-
-
Lister, R.1
Pelizzola, M.2
Dowen, R.H.3
Hawkins, R.D.4
Hon, G.C.5
Tonti-Filippini, J.6
-
21
-
-
84655162785
-
Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains
-
Berman BP, Weisenberger DJ, Aman JF, Hinoue T, Ramjan Z, Liu Y, et al.Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet. 2012; 44:40-6. doi: 10.1038/ng.969.
-
(2012)
Nat Genet
, vol.44
, pp. 40-46
-
-
Berman, B.P.1
Weisenberger, D.J.2
Aman, J.F.3
Hinoue, T.4
Ramjan, Z.5
Liu, Y.6
-
22
-
-
79960927422
-
Increased methylation variation in epigenetic domains across cancer types
-
Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, et al.Increased methylation variation in epigenetic domains across cancer types. Nat Genet. 2011; 43:768-75. doi: 10.1038/ng.865.
-
(2011)
Nat Genet
, vol.43
, pp. 768-775
-
-
Hansen, K.D.1
Timp, W.2
Bravo, H.C.3
Sabunciyan, S.4
Langmead, B.5
McDonald, O.G.6
-
23
-
-
84893711405
-
Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization
-
Hansen KD, Sabunciyan S, Langmead B, Nagy N, Curley R, Klein G, et al.Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization. Genome Res. 2014; 24:177-84. doi: 10.1101/gr.157743.113.
-
(2014)
Genome Res
, vol.24
, pp. 177-184
-
-
Hansen, K.D.1
Sabunciyan, S.2
Langmead, B.3
Nagy, N.4
Curley, R.5
Klein, G.6
-
24
-
-
84897997332
-
GeMes, clusters of DNA methylation under genetic control, can inform genetic and epigenetic analysis of disease
-
Liu Y, Li X, Aryee MJ, Ekström TJ, Padyukov L, Klareskog L, et al.GeMes, clusters of DNA methylation under genetic control, can inform genetic and epigenetic analysis of disease. Am J Hum Genet. 2014; 94:485-95. doi: 10.1016/j.ajhg.2014.02.011.
-
(2014)
Am J Hum Genet
, vol.94
, pp. 485-495
-
-
Liu, Y.1
Li, X.2
Aryee, M.J.3
Ekström, T.J.4
Padyukov, L.5
Klareskog, L.6
-
25
-
-
84990924267
-
Functional normalization of 450k methylation array data improves replication in large cancer studies
-
Fortin JP, Labbe A, Lemire M, Zanke B, Hudson T, Fertig E, et al.Functional normalization of 450k methylation array data improves replication in large cancer studies. Genome Biol. 2014; 15:503. doi: 10.1186/s13059-014-0503-2.
-
(2014)
Genome Biol
, vol.15
, pp. 503
-
-
Fortin, J.P.1
Labbe, A.2
Lemire, M.3
Zanke, B.4
Hudson, T.5
Fertig, E.6
-
26
-
-
84897548625
-
Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays
-
Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, et al.Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays. Bioinformatics. 2014; 30:1363-9. doi: 10.1093/bioinformatics/btu049.
-
(2014)
Bioinformatics
, vol.30
, pp. 1363-1369
-
-
Aryee, M.J.1
Jaffe, A.E.2
Corrada-Bravo, H.3
Ladd-Acosta, C.4
Feinberg, A.P.5
Hansen, K.D.6
-
27
-
-
84925153192
-
The effects of chromatin organization on variation in mutation rates in the genome
-
Makova KD, Hardison RC. The effects of chromatin organization on variation in mutation rates in the genome. Nat Rev Genet. 2015; 16:213-23. doi: 10.1038/nrg3890.
-
(2015)
Nat Rev Genet
, vol.16
, pp. 213-223
-
-
Makova, K.D.1
Hardison, R.C.2
-
28
-
-
84865248380
-
Chromatin organization is a major influence on regional mutation rates in human cancer cells
-
Schuster-Böckler B, Lehner B. Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature. 2012; 488:504-7. doi: 10.1038/nature11273.
-
(2012)
Nature
, vol.488
, pp. 504-507
-
-
Schuster-Böckler, B.1
Lehner, B.2
-
29
-
-
84923358817
-
Cell-of-origin chromatin organization shapes the mutational landscape of cancer
-
Polak P, Karlić R, Koren A, Thurman R, Sandstrom R, Lawrence MS, et al.Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature. 2015; 518:360-4. doi: 10.1038/nature14221.
-
(2015)
Nature
, vol.518
, pp. 360-364
-
-
Polak, P.1
Karlić, R.2
Koren, A.3
Thurman, R.4
Sandstrom, R.5
Lawrence, M.S.6
-
30
-
-
84857111200
-
DNase sensitivity QTLs are a major determinant of human expression variation
-
Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, et al.DNase sensitivity QTLs are a major determinant of human expression variation. Nature. 2012; 482:390-4. doi: 10.1038/nature10808.
-
(2012)
Nature
, vol.482
, pp. 390-394
-
-
Degner, J.F.1
Pai, A.A.2
Pique-Regi, R.3
Veyrieras, J.B.4
Gaffney, D.J.5
-
31
-
-
77957940722
-
The NIH roadmap epigenomics mapping consortium
-
Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, et al.The NIH roadmap epigenomics mapping consortium. Nat Biotechnol. 2010; 28:1045-8. doi: 10.1038/nbt1010-1045.
-
(2010)
Nat Biotechnol
, vol.28
, pp. 1045-1048
-
-
Bernstein, B.E.1
Stamatoyannopoulos, J.A.2
Costello, J.F.3
Ren, B.4
Milosavljevic, A.5
Meissner, A.6
-
32
-
-
84888877924
-
Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
-
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013; 10:1213-18. doi: 10.1038/nmeth.2688.
-
(2013)
Nat Methods
, vol.10
, pp. 1213-1218
-
-
Buenrostro, J.D.1
Giresi, P.G.2
Zaba, L.C.3
Chang, H.Y.4
Greenleaf, W.J.5
-
33
-
-
84937857359
-
Single-cell chromatin accessibility reveals principles of regulatory variation
-
Buenrostro JD, Wu B, Litzenburger UM, Ruff D, Gonzales ML, Snyder MP, et al.Single-cell chromatin accessibility reveals principles of regulatory variation. Nature. 2015; 523:486-90. doi: 10.1038/nature14590.
-
(2015)
Nature
, vol.523
, pp. 486-490
-
-
Buenrostro, J.D.1
Wu, B.2
Litzenburger, U.M.3
Ruff, D.4
Gonzales, M.L.5
Snyder, M.P.6
-
34
-
-
77956873627
-
Tackling the widespread and critical impact of batch effects in high-throughput data
-
Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, et al.Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet. 2010; 11:733-9. doi: 10.1038/nrg2825.
-
(2010)
Nat Rev Genet
, vol.11
, pp. 733-739
-
-
Leek, J.T.1
Scharpf, R.B.2
Bravo, H.C.3
Simcha, D.4
Langmead, B.5
-
35
-
-
77952994784
-
Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types
-
Ryba T, Hiratani I, Lu J, Itoh M, Kulik M, Zhang J, et al.Evolutionarily conserved replication timing profiles predict long-range chromatin interactions and distinguish closely related cell types. Genome Res. 2010; 20:761-70. doi: 10.1101/gr.099655.109.
-
(2010)
Genome Res
, vol.20
, pp. 761-770
-
-
Ryba, T.1
Hiratani, I.2
Lu, J.3
Itoh, M.4
Kulik, M.5
Zhang, J.6
-
37
-
-
79960688508
-
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines
-
Bell JT, Pai AA, Pickrell JK, Gaffney DJ, Pique-Regi R, Degner JF, et al.DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol. 2011; 12:10. doi: 10.1186/gb-2011-12-1-r10.
-
(2011)
Genome Biol
, vol.12
, pp. 10
-
-
Bell, J.T.1
Pai, A.A.2
Pickrell, J.K.3
Gaffney, D.J.4
Pique-Regi, R.5
Degner, J.F.6
-
38
-
-
84895918197
-
The TCGA data portal
-
The TCGA data portal. https://tcga-data.nci.nih.gov/tcga/.
-
-
-
-
39
-
-
79952264847
-
Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells
-
Lister R, Pelizzola M, Kida YS, Hawkins RD, Nery JR, Hon G, et al.Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells. Nature. 2011; 471:68-73. doi: 10.1038/nature09798.
-
(2011)
Nature
, vol.471
, pp. 68-73
-
-
Lister, R.1
Pelizzola, M.2
Kida, Y.S.3
Hawkins, R.D.4
Nery, J.R.5
Hon, G.6
-
40
-
-
84941896220
-
-
Data from Salk Institute. http://neomorph.salk.edu/ips_methylomes/data.html.
-
-
-
-
41
-
-
84904722410
-
Illuminaio: an open source IDAT parsing tool for Illumina microarrays
-
Smith ML, Baggerly KA, Bengtsson H, Ritchie ME, Hansen KD. Illuminaio: an open source IDAT parsing tool for Illumina microarrays. F1000Research. 2013; 2:264. doi: 10.12688/f1000research.2-264.v1.
-
(2013)
F1000Research
, vol.2
, pp. 264
-
-
Smith, M.L.1
Baggerly, K.A.2
Bengtsson, H.3
Ritchie, M.E.4
Hansen, K.D.5
-
42
-
-
84876538609
-
Low-level processing of Illumina Infinium DNA Methylation BeadArrays
-
Triche TJ, Weisenberger DJ, Van Den Berg D, Laird PW, Siegmund KD. Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Res. 2013; 41:90. doi: 10.1093/nar/gkt090.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 90
-
-
Triche, T.J.1
Weisenberger, D.J.2
Van Den Berg, D.3
Laird, P.W.4
Siegmund, K.D.5
-
43
-
-
84915750107
-
ShinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R
-
Fortin JP, Fertig E, Hansen KD. ShinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R. F1000Research. 2014; 3:175. doi: 10.12688/f1000research.4680.1.
-
(2014)
F1000Research
, vol.3
, pp. 175
-
-
Fortin, J.P.1
Fertig, E.2
Hansen, K.D.3
-
44
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009; 10:25. doi: 10.1186/gb-2009-10-3-r25.
-
(2009)
Genome Biol
, vol.10
, pp. 25
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
45
-
-
84873349707
-
Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome
-
McCord RP, Nazario-Toole A, Zhang H, Chines PS, Zhan Y, Erdos MR, et al.Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome. Genome Res. 2013; 23:260-9. doi: 10.1101/gr.138032.112.
-
(2013)
Genome Res
, vol.23
, pp. 260-269
-
-
McCord, R.P.1
Nazario-Toole, A.2
Zhang, H.3
Chines, P.S.4
Zhan, Y.5
-
46
-
-
84890023970
-
Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing
-
Selvaraj S, Dixon JR, Bansal V, Ren B. Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nat Biotechnol. 2013; 31:1111-18. doi: 10.1038/nbt.2728.
-
(2013)
Nat Biotechnol
, vol.31
, pp. 1111-1118
-
-
Selvaraj, S.1
Dixon, J.R.2
Bansal, V.3
Ren, B.4
-
47
-
-
84941890869
-
-
Data from University of Chicago. http://eqtl.uchicago.edu/dsQTL_data/RAW_DATA_HDF5.
-
-
-
-
48
-
-
67649837030
-
Rtracklayer: an R package for interfacing with genome browsers
-
Lawrence M, Gentleman R, Carey VJ. Rtracklayer: an R package for interfacing with genome browsers. Bioinformatics. 2009; 25:1841-2. doi: 10.1093/bioinformatics/btp328.
-
(2009)
Bioinformatics
, vol.25
, pp. 1841-1842
-
-
Lawrence, M.1
Gentleman, R.2
Carey, V.J.3
-
49
-
-
77956627119
-
Redefining CpG islands using hidden Markov models
-
Wu H, Caffo B, Jaffee HA, Irizarry RA, Feinberg AP. Redefining CpG islands using hidden Markov models. Biostatistics. 2010; 11:499-514. doi: 10.1093/biostatistics/kxq005.
-
(2010)
Biostatistics
, vol.11
, pp. 499-514
-
-
Wu, H.1
Caffo, B.2
Jaffee, H.A.3
Irizarry, R.A.4
Feinberg, A.P.5
-
50
-
-
84941893750
-
mixOmics: Omics data integration project
-
R package version 5.0-3
-
Le Cao K-A, Gonzalez I, Dejean S, Rohart F, Monget P, Coquery J, et al.mixOmics: Omics data integration project. 2014. R package version 5.0-3. http://CRAN.R-project.org/package=mixOmics.
-
(2014)
-
-
Le Cao, K.-A.1
Gonzalez, I.2
Dejean, S.3
Rohart, F.4
Monget, P.5
Coquery, J.6
-
51
-
-
84941890849
-
-
CG Hub website. https://cghub.ucsc.edu.
-
-
-
-
52
-
-
28744458859
-
Bioconductor: open software development for computational biology and bioinformatics
-
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, et al.Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004; 5:80. doi: 10.1186/gb-2004-5-10-r80.
-
(2004)
Genome Biol
, vol.5
, pp. 80
-
-
Gentleman, R.C.1
Carey, V.J.2
Bates, D.M.3
Bolstad, B.4
Dettling, M.5
Dudoit, S.6
-
53
-
-
84961289551
-
Orchestrating high-throughput genomic analysis with Bioconductor
-
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, et al.Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015; 12:115-21. doi: 10.1038/nmeth.3252.
-
(2015)
Nat Methods
, vol.12
, pp. 115-121
-
-
Huber, W.1
Carey, V.J.2
Gentleman, R.3
Anders, S.4
Carlson, M.5
Carvalho, B.S.6
-
54
-
-
84864819611
-
The Cancer Genome Atlas
-
The Cancer Genome Atlas. http://cancergenome.nih.gov/.
-
-
-
|