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<!DOCTYPE html>
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<meta name="description" content="Resources of Bioinformatics and Interdisciplinary Technologies (BITs)">
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<!--<h1><img src="/static/image/favicon.png" alt="logo">Computational Biology and Biotechnologies (Yang Lab) <br> <text>on genomics, transcriptomics and genome editing<text></h1>-->
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<h2 class="uk-article-title">Softwares</h2>
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<div class="uk-width-medium-1-2">
<div class="uk-panel uk-panel-box uk-panel-header">
<h2 class="uk-panel-title">CIRCexplorer1</h2>
<p class="uk-article-lead">A combined strategy to identify junction reads from back spliced exons and intron lariats.</p>
<a href="http://www.ncbi.nlm.nih.gov/pubmed/25242744" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://github.com/YangLab/CIRCexplorer" class="uk-icon-button uk-icon-github"></a>
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<div class="uk-width-medium-1-2">
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<h2 class="uk-panel-title">CIRCexplorer2</h2>
<p class="uk-article-lead">CIRCexplorer2 is the successor of CIRCexplorer with plenty of new features to facilitate circular RNA identification and characterization.</p>
<a href="http://genome.cshlp.org/content/early/2016/06/30/gr.202895.115.abstract" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://github.com/YangLab/CIRCexplorer2" class="uk-icon-button uk-icon-github"></a>
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<h2 class="uk-panel-title">CIRCpseudo</h2>
<p class="uk-article-lead">CIRCpseudo is a pipeline to map back-splicing junction sequences for circRNA-derived pseudogenes detection. Using this pipeline, you could previously detect circRNA-derived pseudogenes in genome, after maual check you could do further characterizations for them.</p>
<a href="http://www.ncbi.nlm.nih.gov/pubmed/27021280" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://github.com/YangLab/CIRCpseudo" class="uk-icon-button uk-icon-github"></a>
</div>
</div>
<div class="uk-width-medium-1-2">
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<h2 class="uk-panel-title">CIRCfinder</h2>
<p class="uk-article-lead">CIRCfinder is a pipeline to map junction reads for circular intronic RNAs (ciRNAs). Using this pipeline, you could determine the exact boundaries of interested ciRNAs, so that you could do further characterizations for them.</p>
<a href="http://www.ncbi.nlm.nih.gov/pubmed/24035497" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://github.com/YangLab/CIRCfinder" class="uk-icon-button uk-icon-github"></a>
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<h2 class="uk-panel-title">TERate</h2>
<p class="uk-article-lead">TERate is a computational pipeline to measure transcription elongation rates (TERs) with 4sUDRB-Seq.</p>
<a href="http://www.cell.com/cell-reports/fulltext/S2211-1247(16)30329-1?rss=yes" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://github.com/YangLab/TERate" class="uk-icon-button uk-icon-github"></a>
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<h2 class="uk-panel-title">CLEAR/CIRCexplorer3</h2>
<p class="uk-article-lead">CLEAR is a computational pipeline for circular and linear RNA expression analysis from ribosomal-RNA depleted RNA-seq.</p>
<a href="https://www.sciencedirect.com/science/article/pii/S1672022919301664?via%3Dihub" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://github.com/YangLab/CLEAR" class="uk-icon-button uk-icon-github"></a>
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<h2 class="uk-panel-title">bsRNA-seq-m5C</h2>
<p class="uk-article-lead">bsRNA-seq-m5C is a pipeline for m5C calling.</p>
<a href="https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-020-00769-5" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://github.com/YangLab/bsRNA-seq-m5C" class="uk-icon-button uk-icon-github"></a>
</div>
</div>
<div class="uk-width-medium-1-2">
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<h2 class="uk-panel-title">CSI</h2>
<p class="uk-article-lead">CSI is a pipeline to quantitate RNA pairing capacity of orientation-opposite
complementary sequences across circRNA-flanking introns.</p>
<a href="https://www.tandfonline.com/doi/full/10.1080/15476286.2016.1269999" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://github.com/YangLab/CSI" class="uk-icon-button uk-icon-github"></a>
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<h2 class="uk-panel-title">CIRCshapemapper</h2>
<p class="uk-article-lead">CIRCshapemapper is a pipeline to analyze circSHAPE-MaP for circRNA secondary structure prediction.</p>
<a href="https://www.cell.com/cell/fulltext/S0092-8674(19)30347-2?rss=yes" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://github.com/YangLab/CIRCshapemapper" class="uk-icon-button uk-icon-github"></a>
</div>
</div>
<div class="uk-width-medium-1-2">
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<h2 class="uk-panel-title">RADAR</h2>
<p class="uk-article-lead">RADAR is a pipeline to detect and visualize all possible twelve-types of RNA editing events from RNA-seq datasets.</p>
<a href="https://www.cell.com/cell-reports/fulltext/S2211-1247(20)30700-2" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://github.com/YangLab/RADAR" class="uk-icon-button uk-icon-github"></a>
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</div>
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<h2 class="uk-panel-title">CDCscreen</h2>
<p class="uk-article-lead">CDCscreen is a computational pipeline for Cas13d-mediated circRNA screen to identify functional circular RNAs.</p>
<a href="https://www.nature.com/articles/s41592-020-01011-4" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://github.com/YangLab/CDCscreen" class="uk-icon-button uk-icon-github"></a>
</div>
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<h2 class="uk-panel-title">BEIDOU</h2>
<p class="uk-article-lead">BEIDOU is a Unified toolkit to identify base editor or prime editor induced DNA off-target sites.</p>
<a href="https://www.nature.com/articles/s41556-021-00671-4" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://github.com/YangLab/BEIDOU" class="uk-icon-button uk-icon-github"></a>
</div>
</div>
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<div class="uk-panel uk-panel-box uk-panel-header">
<h2 class="uk-panel-title">CFBI</h2>
<p class="uk-article-lead">CFBI is the custom Perl and Shell scripts for calculating frequencies of base substitutions and indels.</p>
<a href="https://www.nature.com/articles/s41556-021-00671-4" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://github.com/YangLab/CFBI" class="uk-icon-button uk-icon-github"></a>
</div>
</div>
<div class="uk-width-medium-1-2">
<div class="uk-panel uk-panel-box uk-panel-header">
<h2 class="uk-panel-title">SCAPTURE</h2>
<p class="uk-article-lead">SCAPRUTE is a deep learning-embedded pipeline that captures polyadenylation information from 3 prime tag-based RNA-seq of single cells.</p>
<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02437-5" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://github.com/YangLab/SCAPTURE" class="uk-icon-button uk-icon-github"></a>
</div>
</div>
<div class="uk-width-medium-1-2">
<div class="uk-panel uk-panel-box uk-panel-header">
<h2 class="uk-panel-title">deepGPS</h2>
<p class="uk-article-lead">DeepGPS is a multimodal deep learning model which can predict protein subcellular localization by outputting both text labels and protein images simultaneously, with the input of protein sequences.</p>
<a href="https://academic.oup.com/bib/article/26/2/bbaf152/8110879" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://bits.fudan.edu.cn/opengps" class="uk-icon-button uk-icon-github"></a>
</div>
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<h2 class="uk-article-title">Databases</h2>
</div>
</div>
<div class="uk-grid" data-uk-grid-margin>
<div class="uk-width-medium-1-2">
<div class="uk-panel uk-panel-box uk-panel-header">
<h2 class="uk-panel-title">CIRCpedia</h2>
<p class="uk-article-lead">CIRCpedia is an integrative database, aiming to annotating alternative back-splicing and alternative splicing in circRNAs across different cell lines. </p>
<a href="http://genome.cshlp.org/content/early/2016/06/30/gr.202895.115.abstract" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="http://www.picb.ac.cn/rnomics/circpedia/" class="uk-icon-button uk-icon-database"></a>
</div>
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<div class="uk-width-medium-1-2">
<div class="uk-panel uk-panel-box uk-panel-header">
<h2 class="uk-panel-title">CIRCpedia v2</h2>
<p class="uk-article-lead">CIRCpedia v2 is an updated circRNA database with integrated information of circRNA annotation, expression, and conservation.</p>
<a href="http://www.picb.ac.cn/static/publication_pdf/2018_GPB_CIRCpediaV2.pdf" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="http://www.picb.ac.cn/rnomics/circpedia/" class="uk-icon-button uk-icon-database"></a>
</div>
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<div class="uk-width-medium-1-2">
<div class="uk-panel uk-panel-box uk-panel-header">
<h2 class="uk-panel-title">BEable-GPS</h2>
<p class="uk-article-lead">BEable-GPS is a database to profile the accessibility of BEs for targeting pathogenic SNVs and provide gRNA designs for pathogenic SNVs and genomic targets.</p>
<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1839-4" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="http://www.picb.ac.cn/rnomics/BEable-GPS" class="uk-icon-button uk-icon-database"></a>
</div>
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<div class="uk-width-medium-1-2">
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<h2 class="uk-panel-title">PASSpedia</h2>
<p class="uk-article-lead">PASSpedia is an encyclopedia database for PAS analyses and comparison across seven species at single cell resolution.</p>
<a href="https://doi.org/10.1093/gpbjnl/qzaf089" class="uk-icon-button uk-icon-file-text-o"></a>
<a href="https://bits.fudan.edu.cn/PASSpedia/" class="uk-icon-button uk-icon-database"></a>
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<p>Copyright 2012-2024 Bioinformatics and Interdisciplinary Technologies (BITs), Yang Lab. All rights reserved.</p>
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