1,721,025 research outputs found
Pairfq: Pairfq version 0.16.0
No full text<p>Summary of changes in this version:</p>
<ul>
<li>Clean up Unix paths correctly (e.g. '/some/relative/../path' becomes '/some/path').
Fixes #10 on github.</li>
</ul>
<p>See the "Changes" file for more information.</p>
Initial release of RCNA and CollaboratinoViz
No full text<p>Network analysis of research collaborations based on UAMS's ORSP's grant database</p>
Transposome version 0.07.4
No full textAnnotation of transposable element families from unassembled sequence read
SpaceTimeCube3D: First working release, no refactoring
No full text3D Multivariate Space-time Cube implemented using Leapmotion and Three.js
Transposome: Transposome version 0.07.7
No full textA toolkit for annotation of transposable element families from unassembled sequence read
ncRNAScan: A pipeline to identify putative novel ncRNAs from deep sequencing data
No full text<p><a href="http://dx.doi.org/10.5281/zenodo.10308"></a></p>
<p><strong>ncRNAScan</strong> is a pipeline to extract putative novel ncRNAs 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. ncRNAScan uses this data in addition to known gene annotation to extract putative ncRNAs 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 refenrece gene and non coding RNA information to identify putative novel ncRNAs.</p>
<a name="user-content-ioroutine-" class="anchor" href="#ioroutine-"></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>ncRNAScan</strong> Pipeline, IO::Routine module is automatically installed.</p></li>
</ul>
<a name="user-content--ncrnascan-" class="anchor" href="#-ncrnascan-"></a>☲☴ ncRNAScan <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 ncRNAScan 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/ncRNAScan
perl ncRNAScan -setup
</li>
<li>
<p>Documentation:</p>
perl ncRNAScan -h
<p>or</p>
perldoc ncRNAScan
<p>or to get help documentation for individual modules, do:</p>
perl ncRNAScan -h cuff
perl ncRNAScan -h cat
perl ncRNAScan -h get
perl ncRNAScan -h fetch
perl ncRNAScan -h cpc
perl ncRNAScan -h rna
perl ncRNAScan -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>
</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>
</ul>
</li>
</ul>
<a name="user-content-citation" class="anchor" href="#citation"></a>Citation
<p>Konganti, Kranti (2014). ncRNAScan: A pipeline to identify novel ncRNAs from deep sequencing data. ZENODO. <a href="http://dx.doi.org/10.5281/zenodo.10308">10.5281/zenodo.10308</a></p>
<p>Cheers,</p>
<p>BioCoder</p>
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>
- …
