-
1
-
-
84883364264
-
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
-
Anders, S. et al. (2013). Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat. Protoc. , 8, 1765-1786.
-
(2013)
Nat. Protoc.
, vol.8
, pp. 1765-1786
-
-
Anders, S.1
-
2
-
-
84928987900
-
HTSeq-a Python framework to work with highthroughput sequencing data
-
Anders, S. et al. (2015). HTSeq-a Python framework to work with highthroughput sequencing data. Bioinformatics, 31, 166-169.
-
(2015)
Bioinformatics
, vol.31
, pp. 166-169
-
-
Anders, S.1
-
3
-
-
84876884110
-
Dysregulation of the basal RNA polymerase transcription apparatus in cancer
-
Bywater, M. J. et al. (2013). Dysregulation of the basal RNA polymerase transcription apparatus in cancer. Nat. Rev. Cancer, 13, 299-314.
-
(2013)
Nat. Rev. Cancer
, vol.13
, pp. 299-314
-
-
Bywater, M.J.1
-
4
-
-
84877028141
-
Comprehensive molecular portraits of human breast tumours
-
Cancer Genome Atlas Network
-
Cancer Genome Atlas Network. (2012). Comprehensive molecular portraits of human breast tumours. Nature, 490, 61-70.
-
(2012)
Nature
, vol.490
, pp. 61-70
-
-
-
5
-
-
84864222718
-
Automated capture of experiment context for easier reproducibility in computational research
-
Davison, A. (2012). Automated capture of experiment context for easier reproducibility in computational research. Comput. Sci. Eng. , 14, 48-56.
-
(2012)
Comput. Sci. Eng.
, vol.14
, pp. 48-56
-
-
Davison, A.1
-
6
-
-
84871809302
-
STAR: Ultrafast universal RNA-seq aligner
-
Dobin, A. et al. (2012). STAR: ultrafast universal RNA-seq aligner. Bioinformatics, 29, 15-21.
-
(2012)
Bioinformatics
, vol.29
, pp. 15-21
-
-
Dobin, A.1
-
7
-
-
84865790047
-
An integrated Encyclopedia of DNA elements in the human genome
-
ENCODE Project Consortium
-
ENCODE Project Consortium. (2012). An integrated Encyclopedia of DNA elements in the human genome. Nature, 489, 57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
8
-
-
84866127830
-
Identifying ChIP-seq enrichment using MACS
-
Feng, J. et al. (2012). Identifying ChIP-seq enrichment using MACS. Nat. Protoc. , 7, 1728-1740.
-
(2012)
Nat. Protoc.
, vol.7
, pp. 1728-1740
-
-
Feng, J.1
-
9
-
-
77955801615
-
Galaxy: A comphrehensible approach for supporting accessible, reproducible, and transparent computational research in the life sciences
-
Goecks, J. et al. (2010). Galaxy: A comphrehensible approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol. , 11, 1-13.
-
(2010)
Genome Biol.
, vol.11
, pp. 1-13
-
-
Goecks, J.1
-
10
-
-
84911421668
-
Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses
-
Golosova, O. et al. (2014). Unipro UGENE NGS pipelines and components for variant calling, RNA-seq and ChIP-seq data analyses. PeerJ. , 2, 1-15.
-
(2014)
PeerJ.
, vol.2
, pp. 1-15
-
-
Golosova, O.1
-
11
-
-
77958489718
-
Ruffus: A lightweight Python library for computational pipelines
-
Goodstadt, L. (2010). Ruffus: A lightweight Python library for computational pipelines. Bioinformatics, 26, 2778-2779.
-
(2010)
Bioinformatics
, vol.26
, pp. 2778-2779
-
-
Goodstadt, L.1
-
12
-
-
77952567987
-
Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities
-
Heinz, S. et al. (2010). Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell, 38, 576-589.
-
(2010)
Mol. Cell
, vol.38
, pp. 576-589
-
-
Heinz, S.1
-
13
-
-
84867306721
-
Snakemake-A scalable bioinformatics workflow engine
-
Koster, J. and Rahmann, S. (2012). Snakemake-A scalable bioinformatics workflow engine. Bioinformatics, 28, 2520-2522.
-
(2012)
Bioinformatics
, vol.28
, pp. 2520-2522
-
-
Koster, J.1
Rahmann, S.2
-
14
-
-
0037068383
-
Identification of mRNAs differentially-expressed between benign and malignant breast tumour cells
-
Liu, D. et al. (2002). Identification of mRNAs differentially-expressed between benign and malignant breast tumour cells. Br. J. Cancer, 87, 423-431.
-
(2002)
Br. J. Cancer
, vol.87
, pp. 423-431
-
-
Liu, D.1
-
15
-
-
79951475133
-
A decade's perspective on DNA sequencing technology
-
Mardis, E. R. (2011). A decade's perspective on DNA sequencing technology. Nature, 470, 198-203.
-
(2011)
Nature
, vol.470
, pp. 198-203
-
-
Mardis, E.R.1
-
16
-
-
77956295988
-
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
-
McKenna, A. et al. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. , 20, 1297-1303.
-
(2010)
Genome Res.
, vol.20
, pp. 1297-1303
-
-
McKenna, A.1
-
17
-
-
85023602424
-
OncoRep: An n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing
-
Meißner, T. et al. (2014). OncoRep: An n-of-1 reporting tool to support genome-guided treatment for breast cancer patients using RNA-sequencing. bioRxiv.
-
(2014)
BioRxiv
-
-
Meißner, T.1
-
18
-
-
84865226981
-
Next-generation sequencing data interpretation: Enhancing reproducibility and accessibility
-
Nekrutenko, A. and Taylor, J. (2012). Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. Nat. Rev. Genet. , 13, 667-672.
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 667-672
-
-
Nekrutenko, A.1
Taylor, J.2
-
19
-
-
84882729023
-
Harnessing virtual machines to simplify next-generation DNA sequencing analysis
-
Nocq, J. et al. (2013). Harnessing virtual machines to simplify next-generation DNA sequencing analysis. Bioinformatics, 29, 2075-2083.
-
(2013)
Bioinformatics
, vol.29
, pp. 2075-2083
-
-
Nocq, J.1
-
20
-
-
77953176036
-
A scaling normalization method for differential expression analysis of RNA-seq data
-
Robinson, M. D. and Oshlack, A. (2010). A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. , 11, 1-9.
-
(2010)
Genome Biol.
, vol.11
, pp. 1-9
-
-
Robinson, M.D.1
Oshlack, A.2
-
21
-
-
75249087100
-
EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
-
Robinson, M. D. et al. (2010). edgeR: A Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139-140.
-
(2010)
Bioinformatics
, vol.26
, pp. 139-140
-
-
Robinson, M.D.1
-
22
-
-
84861746974
-
Bpipe: A tool for running and managing bioinformatics pipelines
-
Sadedin, S. et al. (2012). Bpipe: A tool for running and managing bioinformatics pipelines. Bioinformatics, 28, 1525-1526.
-
(2012)
Bioinformatics
, vol.28
, pp. 1525-1526
-
-
Sadedin, S.1
-
23
-
-
84856327481
-
Graphite-a Bioconductor package to convert pathway topology to gene network
-
Sales, G. et al. (2012). graphite-a Bioconductor package to convert pathway topology to gene network. BMC Bioinformatics, 13, 20.
-
(2012)
BMC Bioinformatics
, vol.13
, pp. 20
-
-
Sales, G.1
-
24
-
-
58049215467
-
A novel signaling pathway impact analysis
-
Tarca, A. L. et al. (2009). A novel signaling pathway impact analysis. Bioinformatics, 25, 75-82.
-
(2009)
Bioinformatics
, vol.25
, pp. 75-82
-
-
Tarca, A.L.1
-
25
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
-
Trapnell, C. et al. (2012). Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protoc. , 7, 562-578.
-
(2012)
Nat. Protoc.
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
-
26
-
-
77954182362
-
ConsensusClusterPlus: A class discovery tool with confidence assessments and item tracking
-
Wilkerson, M. D. and Hayes, D. N. (2010). ConsensusClusterPlus: A class discovery tool with confidence assessments and item tracking. Bioinformatics, 26, 1572-1573.
-
(2010)
Bioinformatics
, vol.26
, pp. 1572-1573
-
-
Wilkerson, M.D.1
Hayes, D.N.2
-
27
-
-
84882310107
-
The Taverna workflow suite: Designing and executing workflows of Web Services on the desktop, web or in the cloud
-
Wolstencroft, K. et al. (2013). The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud. Nucleic Acids Res. , 41, W557-W561.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. W557-W561
-
-
Wolstencroft, K.1
-
28
-
-
85023612165
-
MyGene. Info: Gene annotation query as a service
-
Wu, C. W. et al. (2014). MyGene. info: gene annotation query as a service. bioRxiv.
-
(2014)
BioRxiv
-
-
Wu, C.W.1
|