| danrer10-gtf-ensembl-v1 | 1 | The GRCz10 gtf file from ensembl remapped to danRer10 (Any unmapped entries are removed from the file) | Mar 25, 2025 | — |
| danrer10-gtf-refseq-ucsc-v1 | 1 | The UCSC RefSeq gene track converted into GTF format containing known zebrafish protein-coding and non-protein-coding genes from RefSeq. (RefSeq: NCBI RNA reference sequence collection) (UCSC GTF format info: https://genome.ucsc.edu/FAQ/FAQformat.html#format3) | Mar 25, 2025 | — |
| danrer10-reference-genome-ucsc-v1 | 1 | The danRer10 reference genome from UCSC | Mar 25, 2025 | — |
| danrer11-reference-genome-ucsc-v1 | 1 | The danRer11 reference genome from UCSC | Mar 25, 2025 | — |
| grch37-1000g-omni-snps-broad-v1 | 1 | The 1000G omni snps vcf file | Mar 25, 2025 | — |
| grch37-1000g-snps-phase1-broad-v1 | 1 | The 1000G high confidence snps from phase 1 in vcf format | Mar 25, 2025 | — |
| grch37-amino-acid-sequences-chr-regions-gencode-v1 | 1 | Protein-coding transcript translation sequences. Amino acid sequences of coding transcript translations on the reference chromosomes | Mar 25, 2025 | — |
| grch37-autosomal-dominant-genes-berg-blekhman-v1 | 1 | CDS region genomic coordinates, along with the compliment coordinates, for combined set of OMIM disease genes deemed to follow autosomal dominant inheritance. (Assembled by Macarthur Lab). Gene sets from: Berg et al, 2013: (https://www.ncbi.nlm.nih.gov/pubmed/22995991). Blekham et al, 2008: (https://www.ncbi.nlm.nih.gov/pubmed/18571414) | Mar 25, 2025 | — |
| grch37-autosomal-dominant-genes-berg-v1 | 1 | CDS region genomic coordinates, along with the compliment coordinates, for OMIM disease genes (as of June 2011) deemed to follow autosomal dominant inheritance. (Assembled by Macarthur Lab). Berg et al, 2013: (https://www.ncbi.nlm.nih.gov/pubmed/22995991). | Mar 25, 2025 | — |
| grch37-autosomal-dominant-genes-blekhman-v1 | 1 | CDS region genomic coordinates, along with the compliment coordinates, for OMIM disease genes deemed to follow autosomal dominant inheritance according to extensive manual curation by Molly Przeworski's group.(https://www.ncbi.nlm.nih.gov/pubmed/18571414). | Mar 25, 2025 | — |
| grch37-autosomal-recessive-genes-berg-blekhman-v1 | 1 | CDS region genomic coordinates, along with the compliment coordinates, for combined set of OMIM disease genes deemed to follow autosomal recessive inheritance. (Assembled by Macarthur Lab). Gene sets from: Berg et al, 2013: (https://www.ncbi.nlm.nih.gov/pubmed/22995991). Blekham et al, 2008: (https://www.ncbi.nlm.nih.gov/pubmed/18571414) | Mar 25, 2025 | — |
| grch37-autosomal-recessive-genes-berg-v1 | 1 | CDS region genomic coordinates, along with the compliment coordinates, for OMIM disease genes (as of June 2011) deemed to follow autosomal recessive inheritance. (Assembled by Macarthur Lab). Berg et al, 2013: (https://www.ncbi.nlm.nih.gov/pubmed/22995991). | Mar 25, 2025 | — |
| grch37-autosomal-recessive-genes-blekhman-v1 | 1 | CDS region genomic coordinates, along with the compliment coordinates, for OMIM disease genes deemed to follow autosomal recessive inheritance according to extensive manual curation by Molly Przeworski's group.(https://www.ncbi.nlm.nih.gov/pubmed/18571414). | Mar 25, 2025 | — |
| grch37-cancer-genes-futreal-v1 | 1 | CDS region genomic coordinates, along with complement coordinates, for a manually curated set of cancer genes from Futreal et al. https://www.nature.com/articles/nrc1299. Gene symbols manually extracted from the supplemental PDF table here: https://media.nature.com/original/nature-assets/nrc/journal/v4/n3/extref/nrc1299-S1.pdf. Gene symbols manually translated to HGNC nomeclature. | Mar 25, 2025 | — |
| grch37-canonical-isoforms-ucsc-v1 | 1 | UCSC defined Canonical Isoform for each gene (or cluster). This tends to be the longest isoform. Remapped from UCSC hg19 to Ensembl GRCh37 | Mar 25, 2025 | — |
| grch37-canonical-transcript-features-ensembl-v1 | 1 | Gene features from Ensembl Release-75 for protein-coding canonical transcripts based on the APPRIS transcript annotations. Features include gene, transcript, CDS, UTR, exon, start_codon, and stop_codon for all canonical transcripts. Canonical transcripts are determined based on APPRIS annotations. 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 annotated by APPRIS are missing from the base gtf file no canonical transcript is chosen and the gene is removed. 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 | Mar 25, 2025 | — |
| grch37-canonical-transcript-features-gencode-v1 | 1 | 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. | Mar 25, 2025 | — |
| grch37-ccdg-sv-vcf-ccdg-v1 | 1 | SV callset 2 from ccdg in grch37 | Mar 25, 2025 | — |
| grch37-ccds-genes-ucsc-v1 | 1 | Consensus Coding Seqeunce (CCDS) high confidence gene annotation from UCSC. The annotation here are high quality manually curated protein-coding regions from the Consensus CDS project. Remapped from UCSC hg19 to Ensembl GRCh37 | Mar 25, 2025 | — |
| grch37-cds-only-features-ensembl-v1 | 1 | CDS only features from Ensembl gene sets. All other features have been removed. (Alignment based annotation using proteins, cDNA, RNA-seq, etc.). Features include: CDS. Features are in GTF format. | Mar 25, 2025 | — |
| grch37-cds-only-features-gencode-v1 | 1 | CDS 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. Some annotations were obtained from GENCODE v19 when mapping failed. Scaffoldings, assenbly patches, and alternative loci are NOT included. Features include: CDS. | Mar 25, 2025 | — |
| grch37-chrom-mapping-ensembl2refseq-ncbi-v1 | 1 | A tab delimited file containing scaffolding ids that maps GRCh37 Ensembl(GenBank) scaffoldings to GRCh37 RefSeq scaffoldings. This is specific to patch 13 of the GRCh37 Human genome build. (1st column = Ensembl ids, 2nd column = RefSeq ids) | Mar 25, 2025 | — |
| grch37-chrom-mapping-refseq2ensembl-ncbi-v1 | 1 | A tab delimited file containing scaffolding ids that maps GRCh37 RefSeq scaffoldings to GRCh37 Ensembl(GenBank) scaffoldings. This is specific to patch 13 of the GRCh37 Human genome build. (1st column = RefSeq ids, 2nd column = Ensembl ids) | Mar 25, 2025 | — |
| grch37-chrom-mapping-ucsc2ensembl-ncbi-v1 | 1 | A tab delimited file containing scaffolding ids that maps hg19 UCSC scafoldings to GRCh37 Ensembl(GenBank) scaffoldings. This is specific to patch 13 of the GRCh37 Human genome build. (1st column = UCSC ids, 2nd column = Ensembl idss) | Mar 25, 2025 | — |
| grch37-chrom-mapping-ucsc2refseq-ncbi-v1 | 1 | A tab delimited file containing scaffolding ids that maps hg19 UCSC scaffoldings to GRCh37 RefSeq scaffoldings. This is specific to patch 13 of the GRCh37 Human genome build. (1st column = UCSC ids, 2nd column = RefSeq ids) | Mar 25, 2025 | — |
