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Dataset results
86 results for “hg38”
SpliceAI_rocksdb_hg38_chrX
<p>SpliceAI RocksDB for chromosome X of hg38 as used in the AbSplice publication: <a href="https://www.nature.com/articles/s41588-023-01373-3">https://www.nature.com/articles/s41588-023-01373-3</a></p> <p>Precomputed SpliceAI scores for all SNVs and indels up to 4 nucleotides are stored in this database. To use this database for fast computation of SpliceAI predictions see: <a href="https://github.com/gagneurlab/spliceai_rocksdb">https://github.com/gagneurlab/spliceai_rocksdb</a></p> <p>This is also implemented in the AbSplice package: <a href="https://github.com/gagneurlab/absplice">https://github.com/gagneurlab/absplice</a></p> <p>This dataset includes SpliceAI scores. The scores are free for academic and not-for-profit use; other use requires a commercial license from Illumina, Inc., see the GitHub repository of SpliceAI: <a href="https://github.com/Illumina/SpliceAI/tree/master">https://github.com/Illumina/SpliceAI/tree/master</a></p>
SpliceAI_rocksdb_hg38_chr20
<p>SpliceAI RocksDB for chromosome 20 of hg38 as used in the AbSplice publication: <a href="https://www.nature.com/articles/s41588-023-01373-3">https://www.nature.com/articles/s41588-023-01373-3</a></p> <p>Precomputed SpliceAI scores for all SNVs and indels up to 4 nucleotides are stored in this database. To use this database for fast computation of SpliceAI predictions see: <a href="https://github.com/gagneurlab/spliceai_rocksdb">https://github.com/gagneurlab/spliceai_rocksdb</a></p> <p>This is also implemented in the AbSplice package: <a href="https://github.com/gagneurlab/absplice">https://github.com/gagneurlab/absplice</a></p> <p>This dataset includes SpliceAI scores. The scores are free for academic and not-for-profit use; other use requires a commercial license from Illumina, Inc., see the GitHub repository of SpliceAI: <a href="https://github.com/Illumina/SpliceAI/tree/master">https://github.com/Illumina/SpliceAI/tree/master</a></p>
SpliceAI_rocksdb_hg38_chr8
<p>SpliceAI RocksDB for chromosome 8 of hg38 as used in the AbSplice publication: <a href="https://www.nature.com/articles/s41588-023-01373-3">https://www.nature.com/articles/s41588-023-01373-3</a></p> <p>Precomputed SpliceAI scores for all SNVs and indels up to 4 nucleotides are stored in this database. To use this database for fast computation of SpliceAI predictions see: <a href="https://github.com/gagneurlab/spliceai_rocksdb">https://github.com/gagneurlab/spliceai_rocksdb</a></p> <p>This is also implemented in the AbSplice package: <a href="https://github.com/gagneurlab/absplice">https://github.com/gagneurlab/absplice</a></p> <p>This dataset includes SpliceAI scores. The scores are free for academic and not-for-profit use; other use requires a commercial license from Illumina, Inc., see the GitHub repository of SpliceAI: <a href="https://github.com/Illumina/SpliceAI/tree/master">https://github.com/Illumina/SpliceAI/tree/master</a></p>
SpliceAI_rocksdb_hg38_chr9
<p>SpliceAI RocksDB for chromosome 9 of hg38 as used in the AbSplice publication: <a href="https://www.nature.com/articles/s41588-023-01373-3">https://www.nature.com/articles/s41588-023-01373-3</a></p> <p>Precomputed SpliceAI scores for all SNVs and indels up to 4 nucleotides are stored in this database. To use this database for fast computation of SpliceAI predictions see: <a href="https://github.com/gagneurlab/spliceai_rocksdb">https://github.com/gagneurlab/spliceai_rocksdb</a></p> <p>This is also implemented in the AbSplice package: <a href="https://github.com/gagneurlab/absplice">https://github.com/gagneurlab/absplice</a></p> <p>This dataset includes SpliceAI scores. The scores are free for academic and not-for-profit use; other use requires a commercial license from Illumina, Inc., see the GitHub repository of SpliceAI: <a href="https://github.com/Illumina/SpliceAI/tree/master">https://github.com/Illumina/SpliceAI/tree/master</a></p>
SpliceAI_rocksdb_hg38_chr5
<p>SpliceAI RocksDB for chromosome 5 of hg38 as used in the AbSplice publication: <a href="https://www.nature.com/articles/s41588-023-01373-3">https://www.nature.com/articles/s41588-023-01373-3</a></p> <p>Precomputed SpliceAI scores for all SNVs and indels up to 4 nucleotides are stored in this database. To use this database for fast computation of SpliceAI predictions see: <a href="https://github.com/gagneurlab/spliceai_rocksdb">https://github.com/gagneurlab/spliceai_rocksdb</a></p> <p>This is also implemented in the AbSplice package: <a href="https://github.com/gagneurlab/absplice">https://github.com/gagneurlab/absplice</a></p> <p>This dataset includes SpliceAI scores. The scores are free for academic and not-for-profit use; other use requires a commercial license from Illumina, Inc., see the GitHub repository of SpliceAI: <a href="https://github.com/Illumina/SpliceAI/tree/master">https://github.com/Illumina/SpliceAI/tree/master</a></p>
SpliceAI_rocksdb_hg38_chr4
<p>SpliceAI RocksDB for chromosome 4 of hg38 as used in the AbSplice publication: <a href="https://www.nature.com/articles/s41588-023-01373-3">https://www.nature.com/articles/s41588-023-01373-3</a></p> <p>Precomputed SpliceAI scores for all SNVs and indels up to 4 nucleotides are stored in this database. To use this database for fast computation of SpliceAI predictions see: <a href="https://github.com/gagneurlab/spliceai_rocksdb">https://github.com/gagneurlab/spliceai_rocksdb</a></p> <p>This is also implemented in the AbSplice package: <a href="https://github.com/gagneurlab/absplice">https://github.com/gagneurlab/absplice</a></p> <p>This dataset includes SpliceAI scores. The scores are free for academic and not-for-profit use; other use requires a commercial license from Illumina, Inc., see the GitHub repository of SpliceAI: <a href="https://github.com/Illumina/SpliceAI/tree/master">https://github.com/Illumina/SpliceAI/tree/master</a></p>
SpliceAI_rocksdb_hg38_chr1
<p>SpliceAI RocksDB for chromosome 1 of hg38 as used in the AbSplice publication: <a href="https://www.nature.com/articles/s41588-023-01373-3">https://www.nature.com/articles/s41588-023-01373-3</a></p> <p>Precomputed SpliceAI scores for all SNVs and indels up to 4 nucleotides are stored in this database. To use this database for fast computation of SpliceAI predictions see: <a href="https://github.com/gagneurlab/spliceai_rocksdb">https://github.com/gagneurlab/spliceai_rocksdb</a></p> <p>This is also implemented in the AbSplice package: <a href="https://github.com/gagneurlab/absplice">https://github.com/gagneurlab/absplice</a></p> <p>This dataset includes SpliceAI scores. The scores are free for academic and not-for-profit use; other use requires a commercial license from Illumina, Inc., see the GitHub repository of SpliceAI: <a href="https://github.com/Illumina/SpliceAI/tree/master">https://github.com/Illumina/SpliceAI/tree/master</a></p>
SpliceAI_rocksdb_hg38_chr6
<p>SpliceAI RocksDB for chromosome 6 of hg38 as used in the AbSplice publication: <a href="https://www.nature.com/articles/s41588-023-01373-3">https://www.nature.com/articles/s41588-023-01373-3</a></p> <p>Precomputed SpliceAI scores for all SNVs and indels up to 4 nucleotides are stored in this database. To use this database for fast computation of SpliceAI predictions see: <a href="https://github.com/gagneurlab/spliceai_rocksdb">https://github.com/gagneurlab/spliceai_rocksdb</a></p> <p>This is also implemented in the AbSplice package: <a href="https://github.com/gagneurlab/absplice">https://github.com/gagneurlab/absplice</a></p> <p>This dataset includes SpliceAI scores. The scores are free for academic and not-for-profit use; other use requires a commercial license from Illumina, Inc., see the GitHub repository of SpliceAI: <a href="https://github.com/Illumina/SpliceAI/tree/master">https://github.com/Illumina/SpliceAI/tree/master</a></p>
SpliceAI_rocksdb_hg38_chr7
<p>SpliceAI RocksDB for chromosome 7 of hg38 as used in the AbSplice publication: <a href="https://www.nature.com/articles/s41588-023-01373-3">https://www.nature.com/articles/s41588-023-01373-3</a></p> <p>Precomputed SpliceAI scores for all SNVs and indels up to 4 nucleotides are stored in this database. To use this database for fast computation of SpliceAI predictions see: <a href="https://github.com/gagneurlab/spliceai_rocksdb">https://github.com/gagneurlab/spliceai_rocksdb</a></p> <p>This is also implemented in the AbSplice package: <a href="https://github.com/gagneurlab/absplice">https://github.com/gagneurlab/absplice</a></p> <p>This dataset includes SpliceAI scores. The scores are free for academic and not-for-profit use; other use requires a commercial license from Illumina, Inc., see the GitHub repository of SpliceAI: <a href="https://github.com/Illumina/SpliceAI/tree/master">https://github.com/Illumina/SpliceAI/tree/master</a></p>
SpliceAI_rocksdb_hg38_chr3
<p>SpliceAI RocksDB for chromosome 3 of hg38 as used in the AbSplice publication: <a href="https://www.nature.com/articles/s41588-023-01373-3">https://www.nature.com/articles/s41588-023-01373-3</a></p> <p>Precomputed SpliceAI scores for all SNVs and indels up to 4 nucleotides are stored in this database. To use this database for fast computation of SpliceAI predictions see: <a href="https://github.com/gagneurlab/spliceai_rocksdb">https://github.com/gagneurlab/spliceai_rocksdb</a></p> <p>This is also implemented in the AbSplice package: <a href="https://github.com/gagneurlab/absplice">https://github.com/gagneurlab/absplice</a></p> <p>This dataset includes SpliceAI scores. The scores are free for academic and not-for-profit use; other use requires a commercial license from Illumina, Inc., see the GitHub repository of SpliceAI: <a href="https://github.com/Illumina/SpliceAI/tree/master">https://github.com/Illumina/SpliceAI/tree/master</a></p>
SpliceAI_rocksdb_hg38_chr2
<p>SpliceAI RocksDB for chromosome 2 of hg38 as used in the AbSplice publication: <a href="https://www.nature.com/articles/s41588-023-01373-3">https://www.nature.com/articles/s41588-023-01373-3</a></p> <p>Precomputed SpliceAI scores for all SNVs and indels up to 4 nucleotides are stored in this database. To use this database for fast computation of SpliceAI predictions see: <a href="https://github.com/gagneurlab/spliceai_rocksdb">https://github.com/gagneurlab/spliceai_rocksdb</a></p> <p>This is also implemented in the AbSplice package: <a href="https://github.com/gagneurlab/absplice">https://github.com/gagneurlab/absplice</a></p> <p>This dataset includes SpliceAI scores. The scores are free for academic and not-for-profit use; other use requires a commercial license from Illumina, Inc., see the GitHub repository of SpliceAI: <a href="https://github.com/Illumina/SpliceAI/tree/master">https://github.com/Illumina/SpliceAI/tree/master</a></p>
hg38 genome data
<p><a href="https://zenodo.org/api/files/16f6e788-a7f7-451f-ab7a-23f2398b85b6/hg38_ctgmin500k.fa.gz">hg38_ctgmin500k.fa.gz</a>:Raw Hg38 genome fasta.</p> <p><a href="https://zenodo.org/api/files/16f6e788-a7f7-451f-ab7a-23f2398b85b6/hg38_ctgmin500k_simulated1.fa.gz">hg38_ctgmin500k_simulated1.fa.gz</a> : Simulated heterozygous hg38 genome.</p> <p><a href="https://zenodo.org/api/files/16f6e788-a7f7-451f-ab7a-23f2398b85b6/hg38_ctgmin500k_simulated1.fa.gz">hg38_ctgmin500k_simulated2.fa.gz</a> : Simulated error-included hg38 genome.</p>
snoRNA core proteins PAR-CLIP data hg38
<p>In this dataset you can find bed file of snoRNA core binding proteins including dyskerin (DKC1), NOP58, NOP56 and fibrillarin (FBL) lifted from hg19 to hg38. NOP58 repA and repB have been merged as single file , as have FBL replicats.</p> <p>Data were made by Kishore et al. 2013 (http://genomebiology.com/2013/14/5/R45), and The Gene Expression Omnibus (GEO) is GSE43666.</p>
pjhop/DNAmCrosshyb: hg38 and hg19 bisulfite-converted genomes (R .rds files)
<p>Bisulfite-converted genomes as used in the <em>DNAmCrosshyb</em> R package (<a href="http://github.com/pjhop/DNAmCrosshyb">github.com/pjhop/DNAmCrosshyb</a>). Data is saved per chromosome in the ‘DNAString’ format as implemented in the Biostrings BioConductor package. The data is saved in the R rds file format and can be read using the ‘readRDS()’ function. Scripts used to generate these data can be found at <a href="https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg19.R">https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg19.R</a> and <a href="https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg38.R">https://github.com/pjhop/DNAmCrosshyb/blob/master/data-raw/bisulfite_convert_hg38.R</a> . See <a href="https://github.com/pjhop/DNAmCrosshyb">https://github.com/pjhop/DNAmCrosshyb</a> for examples on how to map Illumina 450k/EPIC array probes to the bisulfite-converted genomes.</p>
Geographic allele frequency variation in the 1000 Genomes hg38 NYGC dataset
<p>A key challenge in human genetics is to describe and understand the distribution of human genetic variation. Often genetic variation is described by showing rela tionships among populations or individuals, in each case drawing inferences over a large number of variants. Here, we present an alternative representation of human genetic variation that reveals the relative abundance of different allele frequency patterns across populations. This approach allows viewers to easily see several features of human genetic structure: (1) most variants are rare and geographically localized, (2) variants that are common in a single geographic region are more likely to be shared across the globe than to be private to that region, and (3) where two individuals differ, it is most often due to variants that are common globally, regardless of whether the individuals are from the same region or different regions. To guide interpretation of the results, we also apply the visualization to contrasting theoretical scenarios with varying levels of divergence and gene flow. Our variant-centric visualization clarifies the major geographic patterns of human variation and can be used to help correct potential misconceptions about the extent and nature of genetic differentiation among populations.</p>
DOHH2 hg38 CTCF ChIP-seq Dataset filtered for Unique Multiread Mappability
<p>hg38 DOHH2 CTCF ChIP-seq Dataset filtered for Unique Multiread Mappability at a threshold of .75 using Umap</p>
DOHH2 hg38 H3K27ac ChIP-seq Dataset filtered for Unique Multiread Mappability
<p>hg38 DOHH2 H3K27ac ChIP-seq Dataset filtered for Unique Multiread Mappability at a threshold of .75 using Umap</p>
DOHH2 hg38 H3K4me3 ChIP-seq Dataset filtered for Unique Multiread Mappability
<p>hg38 DOHH2 H3K4me3 ChIP-seq Dataset filtered for Unique Multiread Mappability at a threshold of .75 using Umap</p>
DOHH2 hg38 H3K27me3 ChIP-seq Dataset filtered for Unique Multiread Mappability
<p>hg38 DOHH2 H3K27me3 ChIP-seq Dataset filtered for Unique Multiread Mappability at a threshold of .75 using Umap</p>
AbSplice-DNA (hg38)
<p>AbSplice-DNA predicts the probability that a variant causes aberrant splicing in a given tissue. See the publication: <a href="https://www.nature.com/articles/s41588-023-01373-3">https://www.nature.com/articles/s41588-023-01373-3</a>.<br>Here, we provide precomputed AbSplice-DNA scores for 49 human tissues and all possible SNVs genome-wide for hg38. This version contains 19,713 protein coding genes.</p> <p>The folder 'AbSplice_DNA_hg38_snvs' contains all scores.<br>The folder 'AbSplice_DNA_hg38_snvs_high_scores' contains scores above 3 different cutoffs, which have approximately the same recalls as the high, medium and low cutoffs of SpliceAI: </p> <ul> <li>high cutoff (0.2),</li> <li>medium cutoff (0.05),</li> <li>low cutoff (0.01).</li> </ul> <p>AbSplice scores are tissue-specific. In case users require a single score we recommend to use the maximum AbSplice score across tissues.</p> <p>AbSplice-DNA scores can be computed from custom VCF files (including indels) with the python package 'absplice': <a href="https://github.com/gagneurlab/absplice">https://github.com/gagneurlab/absplice</a></p> <p>The uploaded files contain the following columns (for longer description see README of <a href="https://github.com/gagneurlab/absplice">github repository of AbSplice</a>):</p> <ul> <li>Genomic coordinates of the variant: <ul> <li>chrom: Chromosome</li> <li>pos: genomic position</li> <li>ref: reference allele</li> <li>alt: alternative allele</li> <li>gene_id: Ensembl GeneID</li> </ul> </li> <li>AbSplice_DNA_{tissue}: AbSplice score for the given tissue</li> <li>delta_logit_psi_{tissue}: MMSplice + SpliceMap score for a given tissue</li> <li>delta_psi_{tissue}: MMSplice + SpliceMap + Ψ_ref score for a given tissue</li> <li>splice_site_is_expressed_{tissue}: binary feature indicating if a splice site in the vicinity of the variant is expressed for a given tissue</li> <li>delta_score: SpliceAI Delta score (maximum of Delta score (acceptor/donor gain/loss))</li> <li>AbSplice_DNA_max: maximum AbSplice score across tissues for the given variant (this score is only provided in the files of the folder 'AbSplice_DNA_hg38_snvs_high_scores')</li> </ul> <p>This dataset includes SpliceAI scores. The scores are free for academic and not-for-profit use; other use requires a commercial license from Illumina, Inc., see the GitHub repository of SpliceAI: <a href="https://github.com/Illumina/SpliceAI/tree/master">https://github.com/Illumina/SpliceAI/tree/master</a></p>
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