Next: About this document ... Up: ncPRO-seq Annotation and Profiling Previous: Installation of additional softwares   Contents

Bibliography

1

Simon Anders and Wolfgang Huber.
Differential expression analysis for sequence count data.
Genome Biology, 11:R106, 2010.

2

Oliver Bembom.
seqLogo: Sequence logos for DNA sequence alignments.
R package version 1.18.0.

3

P. Brodersen and O. Voinnet.
The diversity of RNA silencing pathways in plants.
Trends Genet., 22:268-280, May 2006.

4

T. R. Dreszer, D. Karolchik, A. S. Zweig, A. S. Hinrichs, B. J. Raney, R. M. Kuhn, L. R. Meyer, M. Wong, C. A. Sloan, K. R. Rosenbloom, G. Roe, B. Rhead, A. Pohl, V. S. Malladi, C. H. Li, K. Learned, V. Kirkup, F. Hsu, R. A. Harte, L. Guruvadoo, M. Goldman, B. M. Giardine, P. A. Fujita, M. Diekhans, M. S. Cline, H. Clawson, G. P. Barber, D. Haussler, and W. James Kent.
The UCSC Genome Browser database: extensions and updates 2011.
Nucleic Acids Res., 40:D918-923, Jan 2012.

5

P. P. Gardner, J. Daub, J. Tate, B. L. Moore, I. H. Osuch, S. Griffiths-Jones, R. D. Finn, E. P. Nawrocki, D. L. Kolbe, S. R. Eddy, and A. Bateman.
Rfam: Wikipedia, clans and the "decimal" release.
Nucleic Acids Res., 39:D141-145, Jan 2011.

6

Robert C Gentleman, Vincent J. Carey, Douglas M. Bates, and others.
Bioconductor: Open software development for computational biology and bioinformatics.
Genome Biology, 5:R80, 2004.

7

M. Ghildiyal and P. D. Zamore.
Small silencing RNAs: an expanding universe.
Nat. Rev. Genet., 10:94-108, Feb 2009.

8

A. Kozomara and S. Griffiths-Jones.
miRBase: integrating microRNA annotation and deep-sequencing data.
Nucleic Acids Res., 39:D152-157, Jan 2011.

9

B. Langmead, C. Trapnell, M. Pop, and S. L. Salzberg.
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Genome Biol., 10:R25, 2009.

10

H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, and R. Durbin.
The Sequence Alignment/Map format and SAMtools.
Bioinformatics, 25:2078-2079, Aug 2009.

11

Erich Neuwirth.
RColorBrewer: ColorBrewer palettes, 2011.
R package version 1.0-5.

12

A. R. Quinlan and I. M. Hall.
BEDTools: a flexible suite of utilities for comparing genomic features.
Bioinformatics, 26:841-842, Mar 2010.

13

R Development Core Team.
R: A Language and Environment for Statistical Computing.
R Foundation for Statistical Computing, Vienna, Austria, 2011.
ISBN 3-900051-07-0.

14

AFA. Smit and R. Hubley.
RepeatModeler Open-1.0.
http://www.repeatmasker.org, 2008-2010.

15

R. J. Taft, C. Simons, S. Nahkuri, H. Oey, D. J. Korbie, T. R. Mercer, J. Holst, W. Ritchie, J. J. Wong, J. E. Rasko, D. S. Rokhsar, B. M. Degnan, and J. S. Mattick.
Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans.
Nat. Struct. Mol. Biol., 17:1030-1034, Aug 2010.

16

Joern Toedling, Constance Ciaudo, Olivier Voinnet, Edith Heard, and Emmanuel Barillot.
girafe - an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads.
Bioinformatics, 26:2902-2903, 2010.