326,356 research outputs found
Using Perl for Statistics: Data Processing and Statistical Computing
No full textIn this paper we show how Perl, an expressive and extensible high-level programming language, with network and ob ject-oriented programming support, can be used in processing data for statistics and statistical computing. The paper is organized in two parts. In Part I, we introduce the Perl programming language, with particular emphasis on the features that distinguish it from conventional languages. Then, using practical examples, we demonstrate how Perl's distinguishing features make it particularly well suited to perform labor intensive and sophisticated tasks ranging from the preparation of data to the writing of statistical reports. In Part II we show how Perl can be extended to perform statistical computations using modules and by "embedding" specialized statistical applications. We provide example on how Perl can be used to do simple statistical analyses, perform complex statistical computations involving matrix algebra and numerical optimization, and make statistical computations more easily reproducible. We also investigate the numerical and statistical reliability of various Perl statistical modules. Important computing issues such as ease of use, speed of calculation, and efficient memory usage, are also considered.
Perl-for-Bioinformatics: lncRNApipe: A pipeline to identify putative novel lncRNAs from deep sequencing data
No full text<p><strong>lncRNApipe</strong> is a pipeline to extract putative novel lncRNAs ab initio, given a list of transcripts in GTF format assembled from deep sequencing data (ex: RNA-Seq) and annotation data.</p>
<p>This pipeline script will bind together the functionality of the tools / scripts: cuffcompare, categorize_ncRNAs.pl, get_unique_features.pl, fetch_seq_from_ucsc.pl, RNAfold, Infernal and Coding Potential Calculator (CPC.sh). Transcriptome construction tools such as Cufflinks produces a set of assembled transcripts in GTF format. lncRNApipe uses this data in addition to known gene annotation to extract putative lncRNAs constructed by the ab initio assemblers. The pipeline relies on the FPKM / RPKM values generated by these assemblers to assess the confidence of the constructed de novo transcripts and validates it against the known reference gene and non coding RNA information to identify putative novel lncRNAs.</p>
<p><strong>The quality of predicted novel lncRNAs highly depends upon the most up-to-date known gene and / or ncRNA annotation file(s) supplied to the pipeline.</strong></p>
<a class="anchor" href="#ioroutine-"><span class="octicon octicon-link"></span></a>IO::Routine <a href="https://travis-ci.org/biocoder/Perl-for-Bioinformatics"></a>
<ul>
<li><p>The scripts use custom <a href="https://github.com/biocoder/Perl-for-Bioinformatics/tree/master/IO-Routine">IO::Routine</a> Perl Module.</p></li>
<li><p>If you are installing <strong>lncRNApipe</strong> Pipeline, IO::Routine module is automatically installed.</p></li>
<li><p>Requires Bio::SeqIO module be installed and available.</p></li>
</ul>
<a class="anchor" href="#-lncrnapipe-"><span class="octicon octicon-link"></span></a>☲☴ lncRNApipe <a href="https://travis-ci.org/biocoder/Perl-for-Bioinformatics"></a>
<ul>
<li><p>Head on to <a href="https://github.com/biocoder/Perl-for-Bioinformatics/tree/master/NGS-Utils">NGS-Utils</a> directory for script list.</p></li>
<li>
<p><strong>Install lncRNApipe and all its dependencies (Mac and Linux):</strong></p>
cd /to/your/preferred/install/path
curl -O https://raw.githubusercontent.com/biocoder/Perl-for-Bioinformatics/master/NGS-Utils/lncRNApipe
perl lncRNApipe -setup
</li>
<li>
<p>Documentation:</p>
perl lncRNApipe -h
<p>or</p>
perldoc lncRNApipe
<p>or to get help documentation for individual modules, do:</p>
perl lncRNApipe -h cuff
perl lncRNApipe -h cat
perl lncRNApipe -h get
perl lncRNApipe -h fetch
perl lncRNApipe -h cpc
perl lncRNApipe -h rna
perl lncRNApipe -h inf
</li>
<li>
<p>Known issues:</p>
<ul>
<li>If pipeline setup fails due to XML::Parser module, you need to install XML parser C libraries.</li>
<li>
<p>On Ubuntu / Debian based Linux distributions, as root user, do:</p>
apt-get install libexpat1 libexpat1-dev
</li>
<li>
<p>On RedHat / Fedora / CentOS based Linux distributions, as root user do:</p>
yum install expat expat-devel
</li>
</ul>
<ul>
<li>
<em><strong>RNAfold:</strong></em> RNAfold is slow and does not work for sequences over 10000bp in length. I am working on including an alternative secondary structure prediction program instead of RNAfold. Meanwhile you may skip running RNAfold module by not issuing the --rnafold option with lncRNApipe.</li>
</ul>
</li>
<li>
<p>Caveats:</p>
<ul>
<li>The pipeline script uses a lot of inherent Linux core utils and has been only tested in BASH shell. </li>
<li>Please use absolute full PATH names. Instead of using lncRNApipe -run ./lncRNApipe_output ..., use
lncRNApipe -run /data/lncRNApipe_output ...
</li>
</ul>
</li>
</ul>
<a class="anchor" href="#citation"><span class="octicon octicon-link"></span></a>Citation
<p>Konganti, Kranti (2015). lncRNApipe: A pipeline to identify putative novel lncRNAs from deep sequencing data. <a href="https://github.com/biocoder/Perl-for-Bioinformatics/releases">https://github.com/biocoder/Perl-for-Bioinformatics/releases</a></p>
<p>Cheers,</p>
<p>BioCoder</p>
Web, Graphics & PerlTk Programming: Best of the Perl Journal
No full textIn its first five years of existence, The Perl Journal (TPJ) became the voice of the Perl community. Every serious Perl programmer subscribed to it, and every notable Perl guru jumped at the opportunity to write for it. TPJ explained critical Perl topics and demonstrated Perl's utility for fields as diverse as astronomy, biology, economics, AI, and games. Back issues were hoarded, or swapped like trading cards. No longer in print format, The Perl Journal remains a proud and timeless achievement of Perl during one of its most exciting periods of development. Web, Graphics & Perl/Tk is the s
A suite of Perl modules for handling microarray data
No full textWe describe PerlMAT, a Perl microarray toolkit providing easy to use object-oriented methods for the simplified manipulation, management and analysis of microarray data. The toolkit provides objects for the encapsulation of microarray spots and reporters, several common microarray data file formats and GAL files. In addition, an analysis object provides methods for data processing, and an image object enables the visualisation of microarray data. This important addition to the Perl developer's library will facilitate more widespread use of Perl for microarray application development within the bioinformatics community. The coherent interface and well-documented code enables rapid analysis by even inexperienced Perl developers. © The Author 2008. Published by Oxford University Press. All rights reserved
Custom Perl Script
No full textThe custom perl script used to extract precursors subjected to CID or HCD from mgf files at the end of the proteome discoverer workflow.</div
PERL : le partage de ressources en langues pour l’innovation pédagogique
No full textInternational audienceLe Pôle d’Elaboration de Ressources Linguistiques (PERL) est un service partagé de l’Université Sorbonne Paris Cité (USPC) dont le but est de développer des formations innovantes en langues en tirant parti du potentiel pédagogique important rendu possible grâce au numérique. La finalité de ce pôle vise le renforcement de la formation en langues pour les étudiant-e-s spécialistes d’autres disciplines (LANSAD) qui est l’un des objectifs de la politique de formation d’USPC. Le PERL, lancé en octobre 2015, regroupe 7 universités et établissements de la ComUE autour de la même volonté de mettre à disposition l’ensemble des ressources pédagogiques sur une plate-forme d’enseignement/apprentissage unique et accessible à tou-te-s les étudiant-e-s et enseignant-e-s des établissements membres d’USPC. Il repose sur quatre phases: l’adaptation de ressources existantes, la création de nouvelles ressources, l’expérimentation/amélioration de ces dernières et pour finir, la formation des enseignant-e-s. Ce projet concerne uniquement des formations hybrides ou 100% en ligne avec tuteur-rice car ses acteur-rice-s envisagent l’enseignement/apprentissage médié par le numérique comme une offre complémentaire avec celle déjà existante en présentiel, et non comme une offre de substitution à cette dernière. Cette complémentarité peut répondre partiellement aux besoins actuels face à la massification de l’université (Coleman, 2008), mais aussi et surtout à des changements structurels et éducatifs dans la société (Miras & Narcy-Combes, 2016). Ces ressources concernent, pour le moment, l’allemand, l’anglais, l’espagnol et le français (FLES) mais d’autres langues sont envisagées. Une phase de création de ressources, lors du 1er semestre de l’année universitaire par 13 concepteur-rices recruté-e-s, nous permet ainsi de tester plus d’une dizaine de formations auprès d’apprenant-e-s LANSAD lors du 2ème semestre de la même année.Cet atelier s’inscrit dans la volonté du projet PERL de partager et de diffuser les ressources produites. Il permettra à la fois de présenter quatre formations de mobilité internationale dans les quatre langues du projet (allemand, anglais, espagnol et français) et mises en place sur la plate-forme moodle du pôle. Cette présentation se focalisera sur une prise en main des formations disponibles, mais aussi une discussion autour des difficultés pédagogiques et techniques que les concepteur-rice-s et/ou tuteur-rice-s ont dû surmonter dans la création puis le tutorat de ces formations. Nous présenterons également les perspectives de ces ressources, de ces formations et du PERL pour l’année 2016-17 qui pourront intéresser les participant-e-s. Nous espérons susciter l’intérêt pour mettre en place et adapter ces formations dans les années à venir mais aussi en créer de nouvelles avec de nouvelles thématiques, de nouveaux publics et de nouvelles langues. Cette action sera sous forme d’atelier présentant notre action innovante afin d’en débattre avec des participants susceptibles d’être intéressés par la mise en œuvre de pratiques analogues (présentation de 10 minutes de chaque projet et débat)
Recommended from our members
"Perl's of wisdom" : "Rabbi" Sam Perl, new models of acculturation, and the "in-between" Jew
No full texttext“‘Perl’s of Wisdom’: ‘Rabbi’ Sam Perl, New Models of Acculturation, and the ‘In-Between’ Jew” examines archival materials from the Dolph Briscoe Center for American History, The Brownsville Herald and El Heraldo de Brownsville to demonstrate how Sam Perl — an Eastern European Jewish immigrant who changed the face of Brownsville, Texas — redefines historical approaches to Jewish acculturation. In this bordertown, Perl not only revitalized the Jewish community when he became the temple’s lay-rabbi, but he also actively united Mexican and Anglo communities both in Brownsville and across the border in its sister city of Matamoros. In Perl’s efforts to simultaneously revitalize his own religious community and the greater social landscape of the border area, Perl proved that he did not need to conform to the expectations of Anglo-Christian identity to succeed. Challenging theories of whiteness studies scholars, Perl never sacrificed his Jewish identity, had a boulevard named after him, and came to be known as “Mr. Brownsville.” Indeed, Perl’s profound impact on the Brownsville-Matamoros community was the result of his ability to occupy an “in-between,” interstitial position that did not require him to blend in with majority cultures; that is, Perl remained distinctly Jewish while simultaneously involving himself in both Anglo and Mexican arenas. Immersing himself in every aspect of bordertown life, Perl occupied multiple roles of community authority, serving as a businessman, rabbi, a Charro Days founder, cultural diplomat, court chaplain and radio host. A close examination of Perl’s life and considerable legacy demonstrates how new acculturation models are needed to better understand the manner in which Jews like Perl have adapted and contributed to dominant cultures.Histor
Custom Perl script for extracting SNPs
No full textPerl program used to extract SNPs. Properly accounts for REFSKIP characters (i.e., "") that result from spliced alignments and seemed to be problematic in more widely available SNP calling packages, such as samtools and varscan
Diffusive author(s), cohesive author: Analysis of S/N (1994)
No full textThis study indicates the ways in which various aspects of the author(s) are brought forth in Dumb type’s performance art, the S/N production. Previous research has suggested a non-hierarchical organization of Dumb type and the absence of a “privileged author” in Dumb type’s collaborative work, S/N. However, the results that I have investigated from member’s interviews on the creative process of S/N along with my analysis of the recorded images of S/N, indicate a different aspect of the author(s). First, S/N was created through, so to speak, the collective ideas of the members of Dumb type. Further, S/N has at least nine quotations from previous performances, installations, and printed writings, besides the work-in-progress technique. Explicating one of the “author functions” as given by Michel Foucault, each text has plural subjects of the author. However, it has been revealed from members’ interviews that Teiji Furuhashi had a decision-making role in selecting the members’ ideas within the performance. Since then, S/N has had plural subjects of creation; however, Furuhashi is one of the subjects of creation along with the “privileged author.” S/N has plural authors (diffusive authors) yet at the same time, it has a “privileged author,” Teiji Furuhashi (cohesive author)
Evolving readable Perl
No full textA program is informally deemed readable, for the purpose
of this experiment, if it is easy for a person to
follow the steps that the program takes to solve the
problem. In this experiment, readability is achieved
by constraining the available syntax for generating solutions.
The Genetic Programming (GP) system created uses
the target language Perl because it is an interpreted,
untyped, robust procedural language which has good
error handling and recovery
- …
