[med-svn] [express] 01/01: Long description is not scientific abstract featuring references so citations were moved to debian/upstream/metadata
Andreas Tille
tille at debian.org
Sun Feb 15 20:21:47 UTC 2015
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository express.
commit d2f6188cea4e098dd1f23e2bf5e3cff8cb1deaf5
Author: Andreas Tille <tille at debian.org>
Date: Sun Feb 15 21:20:58 2015 +0100
Long description is not scientific abstract featuring references so citations were moved to debian/upstream/metadata
---
debian/control | 57 ++++++++++++++++--------------------------
debian/upstream/metadata | 64 ++++++++++++++++++++++++++++++++++++++++--------
2 files changed, 75 insertions(+), 46 deletions(-)
diff --git a/debian/control b/debian/control
index fcc6833..6cf04e3 100644
--- a/debian/control
+++ b/debian/control
@@ -28,7 +28,7 @@ Description: Streaming quantification for high-throughput sequencing
transcript-level RNA-Seq quantification, allele-specific/haplotype
expression analysis (from RNA-Seq), transcription factor binding
quantification in ChIP-Seq, and analysis of metagenomic data. It is
- based on an online-EM algorithm [1] that results in space (memory)
+ based on an online-EM algorithm that results in space (memory)
requirements proportional to the total size of the target sequences and
time requirements that are proportional to the number of sampled
fragments. Thus, in applications such as RNA-Seq, eXpress can accurately
@@ -43,39 +43,24 @@ Description: Streaming quantification for high-throughput sequencing
the performance of eXpress for RNA-Seq data, we have observed that this
efficiency does not come at a cost of accuracy. eXpress is more accurate
than other available tools, even when limited to smaller datasets that
- do not require such efficiency [2]. Moreover, like the Cufflinks program
- [3], eXpress can be used to estimate transcript abundances in multi-
- isoform genes. eXpress is also able to resolve multi-mappings of reads
- across gene families, and does not require a reference genome so that it
- can be used in conjunction with de novo assemblers such as Trinity,
- Oases, or Trans-ABySS. The underlying model is based on previously
- described probabilistic models developed for RNA-Seq [4] but is
- applicable to other settings where target sequences are sampled, and
- includes parameters for fragment length distributions, errors in reads,
- and sequence-specific fragment bias [5].
+ do not require such efficiency. Moreover, like the Cufflinks program,
+ eXpress can be used to estimate transcript abundances in multi-isoform
+ genes. eXpress is also able to resolve multi-mappings of reads across
+ gene families, and does not require a reference genome so that it can be
+ used in conjunction with de novo assemblers such as Trinity, Oases, or
+ Trans-ABySS. The underlying model is based on previously described
+ probabilistic models developed for RNA-Seq but is applicable to other
+ settings where target sequences are sampled, and includes parameters for
+ fragment length distributions, errors in reads, and sequence-specific
+ fragment bias.
.
- eXpress can be used to resolve
- ambiguous mappings in other high-throughput sequencing based
- applications. The only required inputs to eXpress are a set of target
- sequences and a set of sequenced fragments multiply-aligned to them.
- While these target sequences will often be gene isoforms, they need not
- be. Haplotypes can be used as the reference for allele-specific
- expression analysis, binding regions for ChIP-Seq, or target genomes in
- metagenomics experiments. eXpress is useful in any analysis where reads
- multi-map to sequences that differ in abundance.
- .
- [1] Cappé O and Moulines E. (2009). On-line expectation–maximization algorithm
- for latent data models. Journal of the Royal Statistical Society.
- doi:10.1111/j.1467-9868.2009.00698.x
- [2] Roberts A and Pachter L (2012). Streaming fragment assignment for
- real-time analysis of sequencing experiments. Nature Methods.
- doi:10.1038/nmeth.2251
- [3] Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ,
- Salzberg SL, Wold B, Pachter L (2010). Transcript assembly and quantification
- by RNA-Seq reveals unannotated transcripts and isoform switching during cell
- differentiation. Nature Biotechnology. doi:10.1038/nbt.162
- [4] Pachter, L (2011). Models for transcript quantification from RNA-Seq.
- Submitted. arXiv:1104.3889v2
- [5] Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L (2011). Improving
- RNA-Seq expression estimates by correcting for fragment bias. Genome Biology.
- doi:10.1186/gb-2011-12-3-r22
+ eXpress can be used to resolve ambiguous mappings in other
+ high-throughput sequencing based applications. The only required inputs
+ to eXpress are a set of target sequences and a set of sequenced
+ fragments multiply-aligned to them. While these target sequences will
+ often be gene isoforms, they need not be. Haplotypes can be used as the
+ reference for allele-specific expression analysis, binding regions for
+ ChIP-Seq, or target genomes in metagenomics experiments. eXpress is
+ useful in any analysis where reads multi-map to sequences that differ in
+ abundance.
+
diff --git a/debian/upstream/metadata b/debian/upstream/metadata
index 6a8f5af..8d7f565 100644
--- a/debian/upstream/metadata
+++ b/debian/upstream/metadata
@@ -1,11 +1,55 @@
Reference:
- Author: Adam Roberts and Lior Pachter
- Title: Streaming fragment assignment for real-time analysis of sequencing experiments
- Journal: Nature Methods
- Year: 2013
- Volume: 10
- Number: 1
- Pages: 71–73
- DOI: 10.1038/nmeth.2251
- PMID: 23160280
- URL: http://www.nature.com/nmeth/journal/v10/n1/full/nmeth.2251.html
+ - Author: Adam Roberts and Lior Pachter
+ Title: Streaming fragment assignment for real-time analysis of sequencing experiments
+ Journal: Nature Methods
+ Year: 2013
+ Volume: 10
+ Number: 1
+ Pages: 71–73
+ DOI: 10.1038/nmeth.2251
+ PMID: 23160280
+ URL: http://www.nature.com/nmeth/journal/v10/n1/full/nmeth.2251.html
+ - Author: Olivier Cappé and Eric Moulines
+ Title: On-line expectation–maximization algorithm for latent data models
+ Year: 2009)
+ Journal: Journal of the Royal Statistical Society
+ Volume: 71
+ Pages: 593–613
+ DOI: 10.1111/j.1467-9868.2009.00698.x
+ URL: http://onlinelibrary.wiley.com/doi/10.1111/j.1467-9868.2009.00698.x/abstract
+ - Author: Adam Roberts and Lior Pachter
+ Title: Streaming fragment assignment for real-time analysis of sequencing experiments
+ Journal: Nature Methods
+ Year: 2013
+ Volume: 10
+ Number: 1
+ Pages: 71–73
+ DOI: 10.1038/nmeth.2251
+ PMID: 23160280
+ URL: http://www.nature.com/nmeth/journal/v10/n1/full/nmeth.2251.html
+ - Author: Cole Trapnell and Brian A Williams and Geo Pertea and Ali Mortazavi and Gordon Kwan and Marijke J van Baren and Steven L Salzberg and Barbara J Wold and Lior Pachter
+ Title: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
+ Journal: Nature Biotechnology
+ Year: 2010
+ Volume: 28
+ Number: 5
+ Pages: 511–515
+ DOI: 10.1038/nbt.1621
+ PMID: 20436464
+ URL: http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html
+ - Author: Lior Pachter
+ Title: Models for transcript quantification from RNA-Seq
+ Cite-As: arXiv:1104.3889 [q-bio.GN]
+ URL: http://arxiv.org/abs/1104.3889
+ eprint: http://arxiv.org/pdf/1104.3889v2.pdf
+ - Author: Adam Roberts and Cole Trapnell and Julie Donaghey and John L Rinn and Lior Pachter
+ Title: Improving RNA-Seq expression estimates by correcting for fragment bias
+ Journal: Genome Biology
+ Year: 2011
+ Volume: 12
+ Number: 3
+ Pages: R22
+ DOI: 10.1186/gb-2011-12-3-r22
+ PMID: 21410973
+ URL: http://genomebiology.com/2011/12/3/R22
+ eprint: http://genomebiology.com/content/pdf/gb-2011-12-3-r22.pdf
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