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hg38-self-chain-high-identity-ucsc-v1
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public |
High identity, >=90%, Self chain alignments of the human genome with an improved gap scoring system. Genomic coordinates are merged across all overlapping intervals, providing continuous high identity self chain repeat regions. Alignments point out areas of duplication within the human genome, with the exception of the pseudoautosomal regions on X and Y. From the Human Chained Self Alignemnts track on UCSC.
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2025-03-25 |
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hg19-self-chain-high-identity-ucsc-v1
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public |
High identity, >=90%, Self chain alignments of the human genome with an improved gap scoring system. Genomic coordinates are merged across all overlapping intervals, providing continuous high identity self chain repeat regions. Alignments point out areas of duplication within the human genome, with the exception of the pseudoautosomal regions on X and Y. From the Human Chained Self Alignments track on UCSC.
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2025-03-25 |
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grch38-self-chain-high-identity-ucsc-v1
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public |
High identity, >=90%, Self chain alignments of the human genome with an improved gap scoring system. Genomic coordinates are merged across all overlapping intervals, providing continuous high identity self chain repeat regions. Alignments point out areas of duplication within the human genome, with the exception of the pseudoautosomal regions on X and Y. From the Human Chained Self Alignemnts track on UCSC. Remapped from UCSC hg38 to Ensembl GRCh37
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2025-03-25 |
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grch37-self-chain-high-identity-ucsc-v1
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public |
High identity, >=90%, Self chain alignments of the human genome with an improved gap scoring system. Genomic coordinates are merged across all overlapping intervals, providing continuous high identity self chain repeat regions. Alignments point out areas of duplication within the human genome, with the exception of the pseudoautosomal regions on X and Y. From the Human Chained Self Alignemnts track on UCSC. Remapped from UCSC hg19 to Ensembl GRCh37
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2025-03-25 |
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hg38-canonical-transcript-features-gencode-v1
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public |
Protein Coding Canonical Transcript Features for each protein coding gene id from GENCODE's v34 (Ensembl 100) comprehensive set of gene anntotations. Canonical Transcripts are determined using the APPRIS annotation dataset. In short, for all protein coding transcripts, transcripts are filtered based on APPRIS isoform flags. If multiple transcripts of the same gene have equal flags, the isoform with the most exons is chosen. If all transcritps for a gene are not annotated by APPRIS, the transcript with the most exons is chosen as the canonical transcript. APPRIS flag information can be found here: http://appris-tools.org/#/downloads or here: https://uswest.ensembl.org/info/genome/genebuild/transcript_quality_tags.html. Features include: gene, transcript, exon, CDS, UTR, start_codon, stop_codon, and Selenocysteine. Remapped from Ensembl GRCh38 to UCSC hg38. (Scaffoldings wihtout UCSC matches are kept with Ensebml ids)
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2025-03-25 |
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meta-recipe-geo-accession-geo-v1
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public |
A meta-recipe for the Gene Expression Omnibus (GEO) database from NCBI. This meta-recipe contains the instructions for accessing GEO data using GEO Accession IDs. GEO Datasets (GDS), GEO Platforms (GPL), GEO Series (GSE), and GEO Samples (GSM) are all accessible through this meta-recipe. Files downloaded for each type are: (GDS) SOFT files. (GPL) SOFT files and ANNOT files if they exist. (GSE) SOFT file and MATRIX files if they exist. (GSM) The main table file as a .txt file. Additionally, for all 4 types, all supplemental files are downloaded if they exist. Once installed, GEO ID specific recipes will contain ID specific info, such as a summary of the data and a url to the GEO Accession ID specific page. This info can be accessed using 'ggd pkg-info'. To install simply add the '--id' flag with the desired GEO Accession ID when running 'ggd install'. Additional info about GEO can be found at http://www.ncbi.nlm.nih.gov/geo
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2025-03-25 |
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hg19-canonical-transcript-features-gencode-v1
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public |
Protein Coding Canonical Transcript Features for each protein coding gene id from GENCODE's v34 (Ensembl 100) comprehensive set of gene anntotations. Originally created on GRCh38 and mapped to GRCh37 by GENCODE (v34lift37). Some annotations were obtained from GENCODE v19 when mapping failed. Scaffoldings, assenbly patches, and alternative loci are NOT included. Canonical Transcripts are determined using the APPRIS annotation dataset. In short, for all protein coding transcripts, transcripts are filtered based on APPRIS isoform flags. If multiple transcripts of the same gene have equal flags, the isoform with the most exons is chosen. If all transcritps for a gene are not annotated by APPRIS, the transcript with the most exons is chosen as the canonical transcript. APPRIS flag information can be found here: http://appris-tools.org/#/downloads or here: https://uswest.ensembl.org/info/genome/genebuild/transcript_quality_tags.html. Features include: gene, transcript, exon, CDS, UTR, start_codon, stop_codon, and Selenocysteine. Remapped from Ensembl GRCh37 to UCSC hg19
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2025-03-25 |
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grch38-canonical-transcript-features-gencode-v1
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public |
Protein Coding Canonical Transcript Features for each protein coding gene id from GENCODE's v34 (Ensembl 100) comprehensive set of gene anntotations. Canonical Transcripts are determined using the APPRIS annotation dataset. In short, for all protein coding transcripts, transcripts are filtered based on APPRIS isoform flags. If multiple transcripts of the same gene have equal flags, the isoform with the most exons is chosen. If all transcritps for a gene are not annotated by APPRIS, the transcript with the most exons is chosen as the canonical transcript. APPRIS flag information can be found here: http://appris-tools.org/#/downloads or here: https://uswest.ensembl.org/info/genome/genebuild/transcript_quality_tags.html. Features include: gene, transcript, exon, CDS, UTR, start_codon, stop_codon, and Selenocysteine.
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2025-03-25 |
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grch37-canonical-transcript-features-gencode-v1
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public |
Protein Coding Canonical Transcript Features for each protein coding gene id from GENCODE's v34 (Ensembl 100) comprehensive set of gene anntotations. Originally created on GRCh38 and mapped to GRCh37 by GENCODE (v34lift37). Some annotations were obtained from GENCODE v19 when mapping failed. Scaffoldings, assenbly patches, and alternative loci are NOT included. Canonical Transcripts are determined using the APPRIS annotation dataset. In short, for all protein coding transcripts, transcripts are filtered based on APPRIS isoform flags. If multiple transcripts of the same gene have equal flags, the isoform with the most exons is chosen. If all transcritps for a gene are not annotated by APPRIS, the transcript with the most exons is chosen as the canonical transcript. APPRIS flag information can be found here: http://appris-tools.org/#/downloads or here: https://uswest.ensembl.org/info/genome/genebuild/transcript_quality_tags.html. Features include: gene, transcript, exon, CDS, UTR, start_codon, stop_codon, and Selenocysteine.
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2025-03-25 |
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hg38-exome-variants-gnomad-v1
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public |
SNV and INDEL varaints from 125,748 exomes in the gnomAD dataset version 2.1.1 in bcf format. These variants were lifted over from gnomAD v2.1.1 GRCh37 to GRCh38 by the gnomAD group. The file constains all subsets of non-neuro, non-cancer, controls-only, and non-TOPMed samples. Remapped from Ensembl GRCh38 to UCSC hg38
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2025-03-25 |
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hg19-exome-variants-gnomad-v1
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public |
SNV and INDEL varaints from 125,748 exomes in the gnomAD dataset version 2.1.1 in bcf format. The file constains all subsets of non-neuro, non-cancer, controls-only, and non-TOPMed samples. Remapped from Ensembl GRCh37 to UCSC hg19
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2025-03-25 |
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grch38-exome-variants-gnomad-v1
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public |
SNV and INDEL varaints from 125,748 exomes in the gnomAD dataset version 2.1.1 in bcf format. These variants were lifted over from gnomAD v2.1.1 GRCh37 to GRCh38 by the gnomAD group. The file constains all subsets of non-neuro, non-cancer, controls-only, and non-TOPMed samples.
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2025-03-25 |
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grch37-exome-variants-gnomad-v1
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public |
SNV and INDEL varaints from 125,748 exomes in the gnomAD dataset version 2.1.1 in bcf format. The file constains all subsets of non-neuro, non-cancer, controls-only, and non-TOPMed samples.
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2025-03-25 |
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hg38-coding-exons-gencode-v1
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public |
Exon Coding Features. Exons that overlap coding regions in protein coding genes. Features are from the comprehensive set of gene annotations including reference chromosomes, scaffoldings, assembly patches, and alternative loci. All other features, including non-coding exon features and non-protein coding exon features, have been removed. Data is specific to GENCODE Release 34 (Ensembl 100). Features include: exon (exons that overlap coding regions in protein coding genes). Remapped from Ensembl GRCh38 to UCSC hg38.
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2025-03-25 |
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hg38-coding-exons-ensembl-v1
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public |
Exon Coding Features. Exons that overlap coding regions in protein coding genes. Features are from Ensembl gene sets. All other features, including non-coding exon features and non-protein coding exon features, have been removed. (Alignment based annotation using proteins, cDNA, RNA-seq, etc.). Features include: exon (exons that overlap coding regions in protein coding genes). Features are in GTF format. Remapped from Ensembl GRCh38 to UCSC hg38
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2025-03-25 |
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hg19-coding-exons-gencode-v1
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public |
Exon Coding Features. Exons that overlap coding regions in protein coding genes. Features are from the comprehensive set of gene annotations created on GRCh38 and mapped to GRCh37 by GENCODE (v34lift37). All other features, including non-coding exon features and non-protein coding exon features, have been removed. Some annotations were obtained from GENCODE v19 when mapping failed. Scaffoldings, assenbly patches, and alternative loci are NOT included. Features include: exon (exons that overlap coding regions in protein coding genes). Remapped from Ensembl GRCh37 to UCSC hg19
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2025-03-25 |
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hg19-coding-exons-ensembl-v1
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public |
Exon Coding Features. Exons that overlap coding regions in protein coding genes. Features are from Ensembl gene sets. All other features, including non-coding exon features and non-protein coding exon features, have been removed. (Alignment based annotation using proteins, cDNA, RNA-seq, etc.) Features include: exon (exons that overlap coding regions in protein coding genes). Features are in GTF format. Remapped from Ensembl GRCh37 to UCSC hg19
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2025-03-25 |
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grch38-coding-exons-gencode-v1
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public |
Exon Coding Features. Exons that overlap coding regions in protein coding genes. Features are from the comprehensive set of gene annotations including reference chromosomes, scaffoldings, assembly patches, and alternative loci. All other features, including non-coding exon features and non-protein coding exon features, have been removed. Data is specific to GENCODE Release 34 (Ensembl 100). Features include: exon (exons that overlap coding regions in protein coding genes).
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2025-03-25 |
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grch38-coding-exons-ensembl-v1
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public |
Exon Coding Features. Exons that overlap coding regions in protein coding genes. Features are from Ensembl gene sets. All other features, including non-coding exon features and non-protein coding exon features, have been removed. (Alignment based annotation using proteins, cDNA, RNA-seq, etc.). Features include: exon (exons that overlap coding regions in protein coding genes). Features are in GTF format
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2025-03-25 |
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grch37-coding-exons-gencode-v1
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public |
Exon Coding Features. Exons that overlap coding regions in protein coding genes. Features are from the comprehensive set of gene annotations created on GRCh38 and mapped to GRCh37 by GENCODE (v34lift37). All other features, including non-coding exon features and non-protein coding exon features, have been removed. Some annotations were obtained from GENCODE v19 when mapping failed. Scaffoldings, assenbly patches, and alternative loci are NOT included. Features include: exon (exons that overlap coding regions in protein coding genes).
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2025-03-25 |
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grch37-coding-exons-ensembl-v1
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public |
Exon Coding Features. Exons that overlap coding regions in protein coding genes. Features are from Ensembl gene sets. All other features, including non-coding exon features and non-protein coding exon features, have been removed. (Alignment based annotation using proteins, cDNA, RNA-seq, etc.). Features include: exon (exons that overlap coding regions in protein coding genes). Features are in GTF format.
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2025-03-25 |
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hg38-utr-only-features-gencode-v1
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public |
UTR only features from the comprehensive set of gene annotations including reference chromosomes, scaffoldings, assembly patches, and alternative loci. All other features have been removed. UTRs have been designated as 5' UTRs or 3' UTRs based on the coding region and strand of the associated gene. Data is specific to GENCODE Release 34 (Ensembl 100). Features include: five_prime_utr, three_prime_utr. Remapped from Ensembl GRCh38 to UCSC hg38.
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2025-03-25 |
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hg38-utr-only-features-ensembl-v1
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public |
UTR only features from Ensembl gene sets. All other features have been removed. (Alignment based annotation using proteins, cDNA, RNA-seq, etc.). Features include: five_prime_utr, three_prime_utr. Features are in GTF format. Remapped from Ensembl GRCh38 to UCSC hg38
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2025-03-25 |
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hg19-utr-only-features-gencode-v1
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public |
UTR only features from the comprehensive set of gene annotations created on GRCh38 and mapped to GRCh37 by GENCODE (v34lift37). All other features have been removed. UTRs have been designated as 5' UTRs or 3' UTRs based on the coding region and strand of the associated gene. Features include: five_prime_utr, three_prime_utr. Some annotations were obtained from GENCODE v19 when mapping failed. Scaffoldings, assembly patches, and alternative loci are NOT included. Remapped from Ensembl GRCh37 to UCSC hg19
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2025-03-25 |
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hg19-utr-only-features-ensembl-v1
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public |
UTR only features from Ensembl gene sets. All other features have been removed. (Alignment based annotation using proteins, cDNA, RNA-seq, etc.) UTRs have been designated as 5' UTRs or 3' UTRs based on the coding region and strand of the associated gene.Features include: five_prime_utr, three_prime_utr. Features are in GTF format. Remapped from Ensembl GRCh37 to UCSC hg19
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2025-03-25 |
