262,894 research outputs found
2022-nf-core-bytesize-bactopia.pdf
No full textRobert A. Petit III will introduce us to his pipeline Bactopia. A first for bytesize, bactopia is not an nf-core pipeline but is rather influenced by nf-core.
This presentation contains the slides used in his bytesizetalk.</p
Using CORE to research outcome measurement
No full textChris Leach and Mike Lucock have been involved with CORE from its beginning. Jointly responsible for the
development of one of the first large databases of the use of CORE in routine clinical practice, they have
published a number of key papers looking at the relationship between CORE and other outcome measures,
and its use to track client progress during therapy
nf-core/pixelator: nf-core/pixelator v1.1.0
No full text<h2>What's Changed</h2>
<ul>
<li>Important! Template update for nf-core/tools v2.13.1 by @nf-core-bot in https://github.com/nf-core/pixelator/pull/83</li>
<li>Update to pixelator 0.16.2 by @johandahlberg in https://github.com/nf-core/pixelator/pull/84</li>
<li>Remove a workaround for container issues, silence some warnings, update default resources by @fbdtemme in https://github.com/nf-core/pixelator/pull/85</li>
<li>Release pixelator 1.1.0 by @fbdtemme in https://github.com/nf-core/pixelator/pull/86, https://github.com/nf-core/pixelator/pull/87</li>
</ul>
<h3>Software dependencies</h3>
<p>| Dependency | Old version | New version |
| ----------- | ----------- | ----------- |
| <code>pixelator</code> | 0.15.2 | 0.16.2 |</p>
<blockquote>
<p><strong>NB:</strong> Dependency has been <strong>updated</strong> if both old and new version information is present.</p>
<p><strong>NB:</strong> Dependency has been <strong>added</strong> if just the new version information is present.</p>
<p><strong>NB:</strong> Dependency has been <strong>removed</strong> if new version information isn't present.</p>
</blockquote>
<p><strong>Full Changelog</strong>: https://github.com/nf-core/pixelator/compare/1.0.3...1.1.0</p>
zetoc: a Dublin Core based current awareness service
No full textzetoc is a current awareness service for UK Higher and Further Education providing Z39.50 access to the British Library's Electronic Table of Contents database of journal articles and conference papers. The zetoc database, updated daily, may also be searched via a World Wide Web interface. An alerting service provides tables of contents by email for new journal issues when they are loaded. The current version of zetoc is Z39.50 Bath Profile compliant and can provide Dublin Core records encoded in XML in answer to Z39.50 search requests. An enhanced version of zetoc, currently a prototype under development, will hold the data within an XML repository, using Dublin Core as the basis of the metadata schema. This paper describes the encoding of bibliographic records for journal articles and conference papers in Dublin Core, and the interoperability between Dublin Core and other bibliographic standards. Keywords: Dublin Core, bibliographic citations, metadata standards, current awareness
nf-core/pixelator: nf-core/pixelator v1.2.0
No full text<h2>What's Changed</h2>
<ul>
<li>Template update for nf-core/tools v2.14.1 by @fbdtemme in https://github.com/nf-core/pixelator/pull/89</li>
<li>Update pixelator to 0.17.1 by @johandahlberg in https://github.com/nf-core/pixelator/pull/90</li>
<li>Set <code>process_high</code> to use 64GB of RAM and <code>process_high_memory</code> to use 128GB of RAM by @johandahlberg in https://github.com/nf-core/pixelator/pull/91</li>
<li>Minor documentation fixes by @johandahlberg in https://github.com/nf-core/pixelator/pull/92</li>
<li>Improve read renaming by @fbdtemme in https://github.com/nf-core/pixelator/pull/93</li>
<li>Release nf-core/pixelator 1.2.0 by @fbdtemme in https://github.com/nf-core/pixelator/pull/94</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/nf-core/pixelator/compare/1.1.0...1.2.0</p>
Synergy of Human Pol II Core Promoter Elements Revealed by Statistical Sequence Analysis
No full textMotivation: The subject of our paper is bioinformatics analysis of the distinguishing features of human promoter DNA sequences, in particular of synergetic combinations of core promoter elements therein. We suppose that specific scenarios of transcription initiation are essentially related to various particular implementations of the interaction of basal transcription machinery with promoter DNA, depending on the presence and mutual positioning of core promoter elements. Results: In addition to the combinations of core promoter elements previously experimentally confirmed [TATA box and Initiator (Inr), Downstream Promoter Element (DPE) and Inr, and TFIIB recognition element (BRE) and TATA box] we propose other alternate synergetic combinations: BRE and Inr, BRE and DPE, and TATA and DPE with respective models. The suggestion is based on a high statistical significance of the alternate combinations in promoters, comparable with the significance of the known combinations. We also present arguments that the BRE element is statistically more important than previously thought, and suggest possible mechanisms of action of the core elements in the promoters with multiple transcription start sites
nf-core/rnasplice: nf-core/rnasplice 1.0.3
No full text<h2>What's Changed</h2>
<ul>
<li>Move read.table out of loop by @jma1991 in https://github.com/nf-core/rnasplice/pull/121</li>
<li>Stop R converting sample names with '-' in string by @jma1991 in https://github.com/nf-core/rnasplice/pull/124</li>
<li>Patch fix v1.0.3 by @jma1991 in https://github.com/nf-core/rnasplice/pull/125</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/nf-core/rnasplice/compare/1.0.2...1.0.3</p>
nf-core/pixelator: nf-core/pixelator v1.0.1
No full text<h2>[<a href="https://github.com/nf-core/pixelator/releases/tag/1.0.1">1.0.1</a>] - 2023-10-27</h2>
<h3>Enhancements & fixes</h3>
<ul>
<li>[<a href="https://github.com/nf-core/pixelator/pull/66">PR #66</a>] - Add a warning and workaround for singularity & apptainer</li>
<li>Cleanup some linting warnings</li>
<li>Update docker image in RENAME_READS to match the singularity container</li>
</ul>
<h3>Software dependencies</h3>
<p>| Dependency | Old version | New version |
| ----------- | ----------- | ----------- |
| <code>pixelator</code> | 0.15.0 | 0.15.2 |</p>
<blockquote>
<p><strong>NB:</strong> Dependency has been <strong>updated</strong> if both old and new version information is present.</p>
<p><strong>NB:</strong> Dependency has been <strong>added</strong> if just the new version information is present.</p>
<p><strong>NB:</strong> Dependency has been <strong>removed</strong> if new version information isn't present.</p>
</blockquote>
On core stability and extendability
No full textThis paper investigates conditions under which the core of a TU cooperative game is stable. In particular the author extends the idea of extendability to find new conditions under which the core is stable. It is also shown that these new conditions are not necessary for core stability.core stability, stable core, extendability
nf-core/metatdenovo: Metatdenovo first release 1.0.0
No full text<p>Release of nf-core/metatdenovo version 1.0.0</p>
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