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Dataset results
14 results for “gnomAD”
gnomAD polymorphism and de novo mutation data for analysis of mutation rates in highly mutable gene classes
<p>We analyze the human mutation rate in three gene classes (IGK, RNU, and tRNA) which deviate from the expectations of a mutation rate model. We examine the distribution of allele frequencies for SNVs within these genes and we analyze the counts of de novo mutations stratified by whether the SNV was observed or not. </p> <p>{CHR}_IGK_SFS_v2_denovo.gz: allele frequencies, mutation rate estimates, and whether the de novo mutation was observed for IGK, RNU, and tRNA genes. Based on gnomAD v3. </p> <p>{CHR}_indiv_mu.csv: quality information for variants in these gene classes from the 1kg subset of gnomAD.</p> <p>"CHR", "POS", "REF", "ALT", "FILTER", "AC", "AN", "MQRankSum", "pab_max", "VQSLOD", "AB", "PN", "MR", "AR", "MG", "MC", "QUAL"</p> <p>all_variants_chr21_mu_h.csv.gz: all variants from chromosome 21 to use for comparing allele frequencies to those in our gene classes.</p> <p>21_indiv_mu_all.csv.gz: quality information from all variants on chromosome 21 from the 1kg subset of gnomAD to use for comparison with gene classes.</p> <p>"CHR", "POS", "REF", "ALT", "FILTER", "AC", "AN", "MQRankSum", "pab_max", "VQSLOD", "AB", "PN", "MR", "AR", "MG", "MC", "QUAL"</p> <p> </p>
Example variant files and corresponding annotations for GnomAD v3.1.1 on a subset of chromosome 22
<p>Example variant files and corresponding hg38 annotations for `chr22:15518158-20127355`.</p> <p>Sources:</p> <ul> <li><a href="http://dx.doi.org/10.1093/nar/gky955">Gencode v34 (hg38)</a></li> <li><a href="https://doi.org/10.1038/s41586-020-2308-7">GnomAD v3.1.1</a></li> </ul>
gnomAD SQLite database WGS v4.0
<p>This package scales the huge gnomAD files (on average ~120G/chrom) to a SQLite database with a size of <100G and allows scientists to look for various variant annotations present in gnomAD (i.e. Allele Count, Depth, Minor Allele Frequency, etc.). (A query containing 300.000 variants takes ~40s.)</p><p>Find more information on <a href="https://github.com/KalinNonchev/gnomAD_DB">here</a>.</p><p>gnomAD SQLite database WGS v4.0</p>
gnomAD SQLite database WES v4.0
<p>This package scales the huge gnomAD files (on average ~120G/chrom) to a SQLite database with a size of <100G and allows scientists to look for various variant annotations present in gnomAD (i.e. Allele Count, Depth, Minor Allele Frequency, etc.). (A query containing 300.000 variants takes ~40s.)</p><p>Find more information on <a href="https://github.com/KalinNonchev/gnomAD_DB">here</a>.</p><p>gnomAD SQLite database WES v4.0</p>
gnomAD SQLite database V3.1.2
<p>This package scales the huge gnomAD files (on average ~120G/chrom) to a SQLite database with a size of 34G for WGS v2.1.1 (261.942.336 variants) and 98G for WGS v3.1.2 (about 759.302.267 variants), and allows scientists to look for various variant annotations present in gnomAD (i.e. Allele Count, Depth, Minor Allele Frequency, etc. - <a href="https://github.com/KalinNonchev/gnomAD_DB/blob/master/gnomad_db/pkgdata/gnomad_columns.yaml">here</a> you can find all selected features given the genome version). (A query containing 300.000 variants takes ~40s.)</p> <p>It extracts from a gnomAD vcf about 23 variant annotations. You can find further infromation about the exact fields <a href="https://github.com/KalinNonchev/gnomAD_DB/blob/master/gnomad_db/pkgdata/gnomad_columns.yaml">here</a>.</p> <p>gnomAD SQLite database V3.1.2</p>
gnomAD SQLite database WGS v4.1
<div> <div> <div> </div> </div> </div> <div> <p>This package scales the huge gnomAD files (on average ~120G/chrom) to a SQLite database with a size of <100G and allows scientists to look for various variant annotations present in gnomAD (i.e. Allele Count, Depth, Minor Allele Frequency, etc.). (A query containing 300.000 variants takes ~40s.)</p> <p>Find more information on <a href="https://github.com/KalinNonchev/gnomAD_DB">here</a>.</p> <p>gnomAD SQLite database WGS v4.1</p> </div>
gnomAD SQLite database WES v4.1
<div> <div> <div> </div> </div> </div> <div> <p>This package scales the huge gnomAD files (on average ~120G/chrom) to a SQLite database with a size of <100G and allows scientists to look for various variant annotations present in gnomAD (i.e. Allele Count, Depth, Minor Allele Frequency, etc.). (A query containing 300.000 variants takes ~40s.)</p> <p>Find more information on <a href="https://github.com/KalinNonchev/gnomAD_DB">here</a>.</p> <p>gnomAD SQLite database WES v4.1</p> </div>
gnomAD SQLite database V2.1.1
<p>This package scales the huge gnomAD files (on average ~120G/chrom) to a SQLite database with a size of 34G for WGS v2.1.1 (261.942.336 variants) and 99G for WGS v3.1.1 (about 759.302.267 variants), and allows scientists to look for various variant annotations present in gnomAD (i.e. Allele Count, Depth, Minor Allele Frequency, etc. - <a href="https://github.com/KalinNonchev/gnomAD_DB/blob/master/gnomad_db/pkgdata/gnomad_columns.yaml">here</a> you can find all selected features given the genome version). (A query containing 300.000 variants takes ~40s.)</p> <p>It extracts from a gnomAD vcf about 23 variant annotations. You can find further infromation about the exact fields <a href="https://github.com/KalinNonchev/gnomAD_DB/blob/master/gnomad_db/pkgdata/gnomad_columns.yaml">here</a>.</p> <p>gnomAD SQLite database V2.1.1</p>
gnomAD SQLite database V3.1.1
<p>This package scales the huge gnomAD files (on average ~120G/chrom) to a SQLite database with a size of 34G for WGS v2.1.1 (261.942.336 variants) and 99G for WGS v3.1.1 (about 759.302.267 variants), and allows scientists to look for various variant annotations present in gnomAD (i.e. Allele Count, Depth, Minor Allele Frequency, etc. - <a href="https://github.com/KalinNonchev/gnomAD_DB/blob/master/gnomad_db/pkgdata/gnomad_columns.yaml">here</a> you can find all selected features given the genome version). (A query containing 300.000 variants takes ~40s.)</p> <p>It extracts from a gnomAD vcf about 23 variant annotations. You can find further infromation about the exact fields <a href="https://github.com/KalinNonchev/gnomAD_DB/blob/master/gnomad_db/pkgdata/gnomad_columns.yaml">here</a>.</p> <p>gnomAD SQLite database V3.1.1</p>
gnomad_rocksdb
<div> <h1>Gnomad Rocksdb</h1> <a href="https://github.com/MuhammedHasan/gnomad_rocksdb#gnomad-rocksdb"></a></div> <p>Fast look up interface allel frequency of variants from gnomad with rocksdb.</p> <div>https://github.com/MuhammedHasan/gnomad_rocksdb</div>
gnomAD Allele Frequency SQLite database V2.1.1
<p>This package scales the huge gnomAD files (on average ~120G/chrom) to a SQLite database with a size of 56G for WGS v3.1.1 (about 760.000.000 variants), and allows scientists to look for minor allele frequencies of variants really fast (A query containing 300.000 variants takes ~40s.) Look here for more information: https://github.com/KalinNonchev/gnomAD_MAF</p> <p>Genomic variant database</p> <p>gnomAD Allele Frequency SQLite database V2.1.1 for hg19</p>
gnomAD Allele Frequency SQLite database V3.1.1
<p>This package scales the huge gnomAD files (on average ~120G/chrom) to a SQLite database with a size of 56G for WGS v3.1.1 (about 760.000.000 variants), and allows scientists to look for minor allele frequencies of variants really fast (A query containing 300.000 variants takes ~40s.) Look here for more information: https://github.com/KalinNonchev/gnomAD_MAF</p> <p>Genomic - variant database</p> <p>gnomAD Allele Frequency SQLite database V3.1.1 for hg38</p>
tableS7-NOBOX-gnomAD_v4variants_reannotation-Hmz-revised
<p><span>Detailed POI-adjusted reannotation and evaluation of the 2613 <em>NOBOX</em> variants in GnomAD v4.0.0</span></p>
tableS5-NOBOX_POIvariants_reannotation-GnomAD-v4-Hmz-revised
<p><span>Detailed POI-adjusted reclassification of <em>NOBOX</em> variants published in POI cases</span></p>
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