263 research outputs found
Indian look at European classic : Vishal Bhardwaj as the adaptor of William Shakespeare's dramas
No full textArtykuł jest analizą adaptacji dramatów Williama Shakespeare'a autorstwa Vishala Bhardwaja. Autor opisuje inne adaptacje szekspirowskie pojawiające się w indyjskiej kinematografii, następnie opisuje adaptację Makbeta, Otella i Hamleta.The article is an analysis of the adaptation of dramas William Shakespeare's made by Vishal Bhardwaj. The author describes other Shakespearean adaptations appearing in the Indian cinematography. The next describes the adaptation of Macbeth, Othello and Hamlet
CCBR/TRANQUIL: TRANQUIL 0.1.0
No full text<p>This is the first version of TRANQUIL which was deployed on FRCE in 2022.</p>
CHAMPAGNE: CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
No full text<ul>
<li>Fix permissions issues in the CLI. (#167)</li>
</ul>Please cite CHAMPAGNE as below
nf-modules: Reusable modules and subworkflows for CCBR Nextflow pipelines
No full text<p>Our documentation website is now live: <a href="https://ccbr.github.io/nf-modules/">https://ccbr.github.io/nf-modules/</a> (#16)</p>
<h3>New modules</h3>
<ul>
<li>bwa/index</li>
<li>bwa/mem<ul>
<li>also runs samtools sort & outputs index in bai format. (#12)</li>
</ul>
</li>
<li>custom/bam2fastq (#14,#22)</li>
<li>custom/convertsicer (#36)</li>
<li>custom/countfastq (#32)</li>
<li>cutadapt (#11)</li>
<li>khmer/uniquekmers (#7)</li>
<li>picard/samtofastq (#21)</li>
<li>samtools/filteraligned (#13,#20)</li>
<li>samtools/sort (#24,#28)</li>
</ul>
<h3>New subworkflows</h3>
<ul>
<li>custom/filter_blacklist (#17,#27)</li>
</ul>
TRANQUIL: TRna AbundaNce QUantification pIpeLine
No full text<ul>
<li>Redirect the website to the README. (#8, @kelly-sovacool)</li>
<li>Use our custom installation of Python and Snakemake when running the pipeline with SLURM on FRCE. (#9, @kelly-sovacool)</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/CCBR/TRANQUIL/compare/v0.2.0...v0.2.1</p>Please cite TRANQUIL as below
Study of Titanium Dioxide Nanoparticles via Molecular Dynamics Simulations
No full textMolecular dynamics simulations are used to study various aspects of nanoparticles of anatase and rutile, which are the two most abundant polymorphs of titanium dioxide (TiO2). The phenomenon of sintering of nanoparticles is examined via simulation and later compared with phenomenological models designed for micron-sized particles. The effect of particle size, phase, orientation and temperature on the process of nanoparticle sintering is determined. The dipole-dipole interactions and particle orientations are found to play a vital role in nanoparticle sintering. The structure of water in the vicinity of anatase and rutile nanoparticles in ambient and hydrothermal aqueous environment is determined using constant pressure and temperature simulations. The low solubility of TiO2 nanoparticles in water corroborates the results obtained. Molecular dynamics simulations are also used to study phase transformations that occur when two or more TiO2 nanoparticles with different phases interact with each other while sintering. At temperatures in the proximity of nanoparticle melting points, phase transformations to the most stable phase are observed
TRANQUIL: TRna AbundaNce QUantification pIpeLine
No full text<ul>
<li>Now using a changelog to track user-facing changes.</li>
<li>Add a <code>mimseq_flags</code> option to the config file with <code>--local-modomics</code> set so users can customize mimseq flags. (#5, @kelly-sovacool)</li>
<li>Use a Docker container built from a <a href="https://github.com/CCBR/mim-tRNAseq/tree/docker_v1.1.8">custom fork</a> of mimseq v1.1.8. (#5, @kelly-sovacool)</li>
<li>Use upgraded singularity and snakemake modules on FRCE. (#5, @kelly-sovacool)</li>
<li>Get the pipeline version from a version file rather than git commit hash. (#7, @kelly-sovacool)</li>
</ul>
TRANQUIL: TRna AbundaNce QUantification pIpeLine
No full text<ul>
<li>Redirect the website to the README. (#8, @kelly-sovacool)</li>
<li>Use our custom installation of Python and Snakemake when running the pipeline with SLURM on FRCE. (#9, @kelly-sovacool)</li>
</ul>
<p><strong>Full Changelog</strong>: https://github.com/CCBR/TRANQUIL/compare/v0.2.0...v0.2.2</p>Please cite TRANQUIL as below
CHAMPAGNE: CHromAtin iMmuno PrecipitAtion sequencinG aNalysis pipEline
No full text<h3>New features</h3>
<ul>
<li>Find motifs in the genome with Homer. (#142)</li>
<li>Run motif enrichment analysis with MEME. (#142)</li>
<li>Annotate peaks with chipseeker. (#142,#147,#157)</li>
<li>Add preseq complexity curve and fastq screen to multiqc report. (#147)</li>
<li>Support multiple replicates per sample and call consensus peaks on replicates. (#129)<ul>
<li>Optionally normalize p-values with the <a href="https://github.com/CCBR/nf-modules/tree/60d50f4c45a50378cad70b49013f51750617caaa/subworkflows/CCBR/consensus_peaks">CCBR/consensus_peaks</a> subworkflow.</li>
</ul>
</li>
<li>Implement differential peak calling. (#158)<ul>
<li>Optionally specify contrasts via a YAML file. If no file is specified, differential analysis is not performed.</li>
<li>If any sample has only one replicate, run <code>MAnorm</code>, otherwise run <code>diffbind</code>.</li>
</ul>
</li>
<li>Print the recommended citation in bibtex format with <code>champagne --citation</code>. (#153)<ul>
<li>CHAMPAGNE is also now archived in Zenodo with DOI <code>10.5281/zenodo.10516078</code>.</li>
</ul>
</li>
<li>The docs website now has a dropdown menu to select which version to view. The latest release is shown by default. (#170)</li>
</ul>
<h3>Bug fixes</h3>
<ul>
<li>Fix deepTools plots (#144):<ul>
<li>Per sample fingerprint plots instead of per replicate.</li>
<li>Input normalized profile plots.</li>
<li>Protein-coding-only versions of plots.</li>
<li>Ensure sample IDs are sorted. (#150)</li>
</ul>
</li>
<li>Fix a bug where the wrong SICER output file was used for downstream analyses. (#155)</li>
<li>Fix CLI profile on machines other than biowulf & FRCE. (#168)</li>
<li>Fix broken bold styling in documentation website. (#53)</li>
</ul>Please cite CHAMPAGNE as below
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