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Dataset results
19 results for “GREEN-VARAN”
GREEN-VARAN scores resources (CADD GRCh37)
<p>Processed CADD scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh37 version for CADD v.1.4.</p> <p>See: <a href="https://cadd.gs.washington.edu/">https://cadd.gs.washington.edu/</a></p> <p>If you use CADD score annotations with GREEN-VARAN don't forget to cite also the original CADD paper.</p>
GREEN-VARAN scores resources (FATHMM-XF GRCh38)
<p>Processed FATHMM-XF non-coding scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh38 version for FATHMM-XF v2.3 non-coding annotations.</p> <p>See: <a href="http://fathmm.biocompute.org.uk/">http://fathmm.biocompute.org.uk/</a></p> <p>If you use FATHMM-XF score annotations with GREEN-VARAN don't forget to cite also the original FATHMM-XF paper.</p>
GREEN-VARAN scores resources (EIGEN GRCh38)
<p>Processed EIGEN and EIGEN-PC scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh38 version for EIGEN v1.1 non-coding annotations, obtained by coordinates liftover.</p> <p>See: <a href="http://www.columbia.edu/~ii2135/eigen.html">http://www.columbia.edu/~ii2135/eigen.html</a></p> <p>If you use EIGEN score annotations with GREEN-VARAN don't forget to cite also the original EIGEN paper.</p>
GREEN-VARAN additional regions resources
<p>Processed functional regions datasets to be used with GREEN-VARAN</p> <p>This repository contains the GRCh37 and GRCh38 files as indexed BED files. The GRCh38 version of UCNE and TAD were obtained by coordinate liftover.</p> <ul> <li>TFBS from ENCODE v3</li> <li>DNase hypersensitivity peaks from ENCODE v3</li> <li>UCNE (ultra-conserved non-coding elements) from https://ccg.epfl.ch/UCNEbase/</li> <li>TAD (topologically associating chromatin domains) from http://dna.cs.miami.edu/TADKB/</li> <li>Super enhancer from dbSuper at http://bioinfo.au.tsinghua.edu.cn/dbsuper/</li> </ul> <p>Please refer to the original datasets listed in related identifiers and references for eventual limits in use and distribution</p>
GREEN-VARAN scores resources (ncER)
<p>Processed ncER scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh37 and GRCh38 versions for ncER v2 single-base resolution annotations. GRCh38 file is obtained by coordinates liftover.</p> <p>Original scores obtained from: https://github.com/TelentiLab/ncER_datasets </p> <p>Original publication: https://www.nature.com/articles/s41467-019-13212-3</p> <p>If you use ncER score annotations with GREEN-VARAN don't forget to cite also the original ncER paper.</p>
GREEN-VARAN scores resources (DANN GRCh37)
<p>Processed DANN scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh37 version for DANN.</p> <p>See: <a href="https://academic.oup.com/bioinformatics/article/31/5/761/2748191">https://academic.oup.com/bioinformatics/article/31/5/761/2748191</a></p> <p>If you use DANN score annotations with GREEN-VARAN don't forget to cite also the original DANN paper.</p>
GREEN-VARAN scores resources (EIGEN GRCh37)
<p>Processed EIGEN and EIGEN-PC scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh37 version for EIGEN v1.1 non-coding annotations.</p> <p>See: <a href="http://www.columbia.edu/~ii2135/eigen.html">http://www.columbia.edu/~ii2135/eigen.html</a></p> <p>If you use EIGEN score annotations with GREEN-VARAN don't forget to cite also the original EIGEN paper.</p>
GREEN-VARAN scores resources (FATHMM-XF GRCh37)
<p>Processed FATHMM-XF non-coding scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh37 version for FATHMM-XF v2.3 non-coding annotations.</p> <p>See: <a href="http://fathmm.biocompute.org.uk/">http://fathmm.biocompute.org.uk/</a></p> <p>If you use FATHMM-XF score annotations with GREEN-VARAN don't forget to cite also the original FATHMM-XF paper.</p>
GREEN-VARAN scores resources (FATHMM-MKL GRCh37)
<p>Processed FATHMM-MKL scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh37 version for FATHMM-MKL v2.3 non-coding annotations.</p> <p>See: <a href="http://fathmm.biocompute.org.uk/">http://fathmm.biocompute.org.uk/</a></p> <p>If you use FATHMM-MKL score annotations with GREEN-VARAN don't forget to cite also the original FATHMM-MKL paper.</p>
GREEN-VARAN scores resources (CADD GRCh38)
<p>Processed CADD scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh38 version for CADD v.1.5.</p> <p>See: <a href="https://cadd.gs.washington.edu/">https://cadd.gs.washington.edu/</a></p> <p>If you use CADD score annotations with GREEN-VARAN don't forget to cite also the original CADD paper.</p>
GREEN-VARAN scores resources (FIRE GRCh37)
<p>Processed FIRE scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh37 version for FIRE.</p> <p>See: <a href="https://sites.google.com/site/fireregulatoryvariation/">https://sites.google.com/site/fireregulatoryvariation/</a></p> <p>If you use FIRE score annotations with GREEN-VARAN don't forget to cite also the original FIRE paper.</p>
GREEN-VARAN scores resources (FATHMM-MKL GRCh38)
<p>Processed FATHMM-MKL scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh38 version for FATHMM-MKL v2.3 non-coding annotations.</p> <p>See: <a href="http://fathmm.biocompute.org.uk/">http://fathmm.biocompute.org.uk/</a></p> <p>If you use FATHMM-MKL score annotations with GREEN-VARAN don't forget to cite also the original FATHMM-MKL paper.</p>
GREEN-VARAN scores resources (GRCh37)
<p>Processed non-coding prediction scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh37 version for the following scores:</p> <ul> <li>ReMM v0.3.1 (<a href="https://charite.github.io/software-remm-score.html">https://charite.github.io/software-remm-score.html</a>)</li> <li>NCBoost v.1 (<a href="https://github.com/RausellLab/NCBoost">https://github.com/RausellLab/NCBoost</a>)</li> <li>ExPECTO (<a href="https://hb.flatironinstitute.org/expecto/">https://hb.flatironinstitute.org/expecto/</a>)</li> <li>LinSight (<a href="https://github.com/CshlSiepelLab/LINSIGHT">https://github.com/CshlSiepelLab/LINSIGHT</a>)</li> <li>GWAVA v1.0 (<a href="https://www.sanger.ac.uk/sanger/StatGen_Gwava">https://www.sanger.ac.uk/sanger/StatGen_Gwava</a>)</li> </ul> <p>If you use any of these score annotations with GREEN-VARAN please cite also the corresponding paper.</p>
GREEN-VARAN AF resources
<p>This dataset contains processed files from gnomAD that can be used with GREEN-VARAN. These files represent the genome-wide variants from gnomAD, but INFO fields have been subset to contain just essential AF annotations.</p> <ul> <li>GRCh37 version is adapted from gnomAD v2.1.1 genome VCF</li> <li>GRCh38 version is adapted from gnomAD v3 genome VCF</li> </ul> <p>See: <a href="https://gnomad.broadinstitute.org/">https://gnomad.broadinstitute.org/</a></p> <p>If you use gnomAD AF annotations with GREEN-VARAN don't forget to cite also the original gnomAD paper as described in <a href="https://gnomad.broadinstitute.org/terms">https://gnomad.broadinstitute.org/terms</a>.</p>
GREEN-VARAN scores resources (DANN GRCh38)
<p>Processed DANN scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh38 version for DANN.</p> <p>See: <a href="https://academic.oup.com/bioinformatics/article/31/5/761/2748191">https://academic.oup.com/bioinformatics/article/31/5/761/2748191</a></p> <p>If you use DANN score annotations with GREEN-VARAN don't forget to cite also the original DANN paper.</p>
GREEN-VARAN scores resources (FIRE GRCh38)
<p>Processed FIRE scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh38 version for FIRE.</p> <p>See: <a href="https://sites.google.com/site/fireregulatoryvariation/">https://sites.google.com/site/fireregulatoryvariation/</a></p> <p>If you use FIRE score annotations with GREEN-VARAN don't forget to cite also the original FIRE paper.</p>
GREEN-VARAN scores resources (GRCh38)
<p>Processed non-coding prediction scores to be used with GREEN-VARAN</p> <p>This dataset contains the GRCh38 version for the following scores. When not available from the original source, the GRCh38 coordinates were obtained by liftover.</p> <ul> <li>ReMM v0.3.1 (<a href="https://charite.github.io/software-remm-score.html">https://charite.github.io/software-remm-score.html</a>)</li> <li>NCBoost v.1 (<a href="https://github.com/RausellLab/NCBoost">https://github.com/RausellLab/NCBoost</a>)</li> <li>ExPECTO (<a href="https://hb.flatironinstitute.org/expecto/">https://hb.flatironinstitute.org/expecto/</a>)</li> <li>LinSight (<a href="https://github.com/CshlSiepelLab/LINSIGHT">https://github.com/CshlSiepelLab/LINSIGHT</a>)</li> <li>GWAVA v1.0 (<a href="https://www.sanger.ac.uk/sanger/StatGen_Gwava">https://www.sanger.ac.uk/sanger/StatGen_Gwava</a>)</li> </ul> <p>If you use any of these score annotations with GREEN-VARAN please cite also the corresponding paper.</p>
GREEN-VARAN SV annotation resources
<p>This dataset contains a collection of BED files prepared to be used with the SV_annotation tool, part of GREEN-VARAN.</p> <p><strong>GREEN-DB regions</strong></p> <p>Regulatory regions collected in GREEN-DB (see <a href="https://github.com/edg1983/GREEN-VARAN">https://github.com/edg1983/GREEN-VARAN</a>)</p> <p><strong>Population AF annotations</strong></p> <p>These files represent SVs from gnomAD v.2.1.1, 1000G phase3, and the IMH dataset. When not directly available, the GRCh38 versions are obtained by coordinates liftover from GRCh37.</p> <p>If you use AF annotations don't forget to cite also the original papers:</p> <ul> <li>gnomAD paper as described in <a href="https://gnomad.broadinstitute.org/terms">https://gnomad.broadinstitute.org/terms</a></li> <li>1000G SV paper: <a href="https://www.nature.com/articles/nature15394">https://www.nature.com/articles/nature15394</a></li> <li>the original IMH publication <a href="https://www.nature.com/articles/s41586-020-2371-0">https://www.nature.com/articles/s41586-020-2371-0</a></li> </ul> <p><strong>Gene annotations</strong></p> <p>Genes and CDSs annotations are from GENCODE v33 basic set</p>
GREEN-VARAN scores resources (PhyloP100)
<p>This dataset contains processed BED files for the PhyloP100 conservation values to be used with GREEN-VARAN annotation tool.</p> <p>PhyloP100 values are available for GRCh37 and GRCh38 genome builds.</p> <p> </p>
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