ABC of cellular microRNAome
Advanced BarChart configuration of cellular microRNAome. Evaluation of >20 billion small RNA-seq reads from 196 primary cell types (+plasma, +platelets) across 175 main studies.
NCBI's Allele Frequency Aggregator (ALFA) allele frequency for variants in dbGaP studies.
Bird Alignment (363 species)
Bird Alignment (363 species)
[+] Gallus_gallus, Acanthisitta_chloris...
Bird genome assemblies
[+] GCA_009769605.1, GCA_009769595.1...
Blueprint Epigenomics Data Hub
DNA methylation, chromatin accessibility, and gene expression data from NeuN flow-sorted human brain samples
Breast Cancer lncRNA
Breast Cancer lncRNA PMID 26236012
Broad Improved Canine Annotation v1
Broad Institute CanFam3 Improved Annotation Data v1
C. elegans wild isolate assembly hub
CADD Track for v1.3 to v1.6
Cancer Genomics Tracks
TCGA and ICGC Cancer Mutations, TCGA Expression, Immune Epitopes Database (IEDB), Cancer Immunity Peptides Database, Dienstmann Variant/Cancer database, CIVIC, MyCancerGenome.org, OncoKB
Epigenomic Data tracks from BCGSC, Vancouver, B.C.
CESAR Gene Mappings
Human Exons mapped by CESAR
[+] bosTau7, ailMel1, allMis1, anoCar2, calJac3...
ChIP-seq data track HUBs from MSC cells from GSE79815
ChIP-seq data from the publication "Epigenetic plasticity drives adipogenic and osteogenic differentiation of marrow-derived mesenchymal stem cells" (10.1074/jbc.M116.736538) from GEO record GSE79815
Colocalized segments of human genome for Roadmap cell types
Cotney Lab Human Craniofacial Epigenomics
Human Embryonic Craniofacial Tissue Epigenomic Data and Chromatin State Segmentations from the Cotney Lab at UConn Health
hg19, mm9, hg38
Cotney Lab Human Embryonic Heart Hub
Human Embryonic Heart Tissue Epigenomic and Transcriptomic Data from the Cotney Lab at UConn Health
COVID-19 Gene Annotation
GENCODE annotation of COVID-19 associated genes
Croc and Bird Hub
Croc, Bird, and Archosaur Assembly Hub
[+] allMis2, Anc00, Anc01, Anc02, Anc03, Anc04, Anc06...
DANIO-CODE Track Hub
DANIO-CODE: Central repository for zebrafish genomic datasets
DASHR small ncRNA Hub
DASHR Human small non-coding RNA data
DASHR v2.0 Hub
DASHR v2.0 Human small non-coding RNA data hub
"dbRIP: Database of Polymorphic and Species-specific Retrotransposons in Humans"
NCBI's database of human genomic Structural Variation -- large variants >50 bp
Dfam database of TE families and annotations
Dfam database of Transposable Element families and genome annotations
Digital genomic footprinting (Vierstra et al., 2020)
Digital genomic footprinting from 243 cell & tissue types
Hundreds of analyzed methylomes from bisulfite sequencing data
[+] hg38, hg19, hg18, mm9, mm10, panTro2, panTro4, ponAbe2...
ENCODE Analysis Hub
ENCODE Integrative Analysis Data Hub
ENCODE DNA Trackhub
ENCODE Trackhub for DNA-based assays
hg19, hg38, mm10
ENCODE integrative Trackhub
ENCODE Trackhub for integrative results
ENCODE RNA Trackhub
ENCODE Trackhub for RNA-based assays
hg19, hg38, mm10
Ensembl Regulatory Build
Evidence summaries and provisional results for the new Ensembl Regulatory Build
hg38, hg19, mm10
EPD Viewer Hub
Promoter specific experimental data and TSS annotation from the EPD database
[+] hg19, hg38, mm9, mm10, danRer7, rheMac8, galGal5, rn6...
Exp/Meth VNTR hub
Association of VNTRs with Expression and Methylation in GTEx, PCGC and PPMI
Eye tissue specific genes and markers, derived from NEIBank and other sources
[+] hg19, bosTau6, canFam2, cavPor3, danRer6, danRer7...
Comprehensive craniofacial research data from FaceBase.org
mm9, mm10, hg18, hg19
RIKEN FANTOM5 Phase1 and Phase2 data
hg38, mm10, hg19, mm9, canFam3, rn6, rheMac8, galGal5
FANTOM5 CAGE RECLU DATA
RIKEN FANTOM5 CAGE clusters by RECLU
Fish genome assemblies
[+] GCF_017589495.1, GCF_000485575.1...
Fungi genome assemblies
[+] GCF_003184765.1, GCF_001890905.1...
GENCODE Annotation Updates
Updates to GENCODE manual annotation since last release
hg38, mm39, mm10
An integrated compendium of ncRNA genes in GeneCards
GeneHancer: genome-wide integration of regulatory elements and target genes in GeneCards
Golden Hamster genome
Genome assembly of Golden Hamster(Mesocricetus auratus) from Siomi lab
GRC Genome Issues under Review
Genome Reference Consortium: Genome issues and other features
hg38, hg19, mm10, mm9, danRer7, danRer10, danRer11
GTEx Analysis Hub
Genotype Tissue Expression (GTEx) Project Analysis Hub
GTEx RNA-seq Signal Hub
RNA-seq read coverage in 53 tissues from GTEx V6 (7572 samples)
Human cellular microRNAome
microRNA RNA-seq based data from 46 primary cell types and 42 cancer or immortalized cell lines.
Human cellular microRNAome barCharts
Evaluation of >10 billion small RNA-seq reads from 78 primary cell types and 42 cancer or immortalized cell lines from 3 main studies.
Human Global Reference Genomes
Human Global Reference Genome assembly hub
Human Islet lncRNAs
ERROR: Couldn't open http://www.imperial.ac.uk/medicine/beta-cell-genome-regulation-laboratory/data/HILNCs/HILNCs.txt Debug Help hg19
human p53 Binding And Expression Resource (BAER) hub
human p53 ChIP-seq coverage depth (tracks) & SISSRs peak calls with associated differential gene expression from published data as of May 2015
human T2T-CHM13 v2.0
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Couldn't open https://hgdownload.soe.ucsc.edu/hubs/GCA/009/914/755/GCA_009914755.4/hub.txt Debug Help GCA_009914755.4
IDEAS roadmap 20states
Roadmap Epigenomics 20 state genome segmentation using the IDEAS algorithm
Invertebrate genome assemblies
[+] GCA_905333045.1, GCF_000005575.2...
TFBS predictions for profiles in the JASPAR CORE collections
[+] hg19, hg38, ce10, ce11, ci3, dm6, sacCer3, danRer10...
LIBD Human DLPFC Development
RNAseq data across human brain development by age group from LIBD
ERROR: Couldn't open https://www.lncipedia.org/trackhub/hub.txt Debug Help hg19, hg38
Mammal and Bird Alignment (605 species)
Mammal and Bird Alignment (605 species)
[+] Homo_sapiens, Gallus_gallus...
Mammal genome assemblies
[+] GCF_000298275.1, GCA_011750645.1...
McGill EMC (CEEHRC)
McGill Epigenomics Mapping Centre, Montreal, Quebec, Canada
MGI Alleles and Phenotypes
Allele's and Phenotypes from the Mouse Genome Informatics (MGI) consortium
miRcode microRNA sites
ERROR: TCP non-blocking connect() to www.mircode.org IP 126.96.36.199 timed-out in select() after 10000 milliseconds - Cancelling!
Couldn't open http://www.mircode.org/ucscHub/hub.txt Debug Help hg19
Cohesin(Smc1)-associated chromatin interactions in murine embryonic stem cells
Mouse strain assemblies
Assembly and alignment data for 16 different mouse strains plus rat.
[+] mm10, rn6, 129S1_SvImJ, WSB_EiJ, SPRET_EiJ, AKR_J...
RNA-Seq, Ribo_Seq, and ORF Predictions
Peptide evidences CNIO
Peptides detected from a re-analysis of multiple experiments and databases
[+] sacCer3, 1B_D1606_spades...
Evolutionary protein-coding potential as measured by PhyloCSF
[+] hg19, hg38, mm10, mm39, galGal4, galGal6, dm6, ce11...
Evolutionary protein-coding potential as measured by PhyloCSF++
rn6, fr3, gasAcu1, tarSyr2, sacCer3
Plant genome assemblies
[+] GCF_001190045.1, GCF_000442705.1...
Very Short Tandem Repeats (MNR/DNR/TNR)
hg38, mm10, rn6, dm6
Primate genome assemblies
[+] GCF_000951035.1, GCA_004027145.1...
Primate x4 NeuroDiff and Human CRISPRa
RNAseq coverage tracks from 4 Primate neuro-differentiation assays and a human CRISPRa assay
hg19, panTro4, ponAbe2, rheMac8
Principal Splice Isoforms APPRIS
Selects a single CDS variant for each gene as the 'PRINCIPAL' isoform based on the range of protein features.
[+] hg38, hg19, mm10, danRer10, rn6, susScr3, panTro4, dm6...
Promoterome CAGE and nucleosome positioning
Zebrafish promoterome based on Haberle et al. and Nepal et al.
Purple sea star Assembly Hub
This is the Assembly Hub of the purple sea star (Pisaster ochraceus, assembly 12Jun2017_28pcJ)
NCBI RefSeq Functional Elements interactions and features
GCA_009914755.4, hg19, hg38, mm10, mm39
ReMap 2018 Regulatory Atlas
ReMap 2018: An atlas of regulatory regions from an integrative analysis of Human DNA-binding sequencing experiments. Go to ReMap for more info. Pubmed link.
ReMap 2020 Regulatory Atlas
ReMap 2020: An atlas of regulatory regions from an integrative analysis of Human and Arabidopsis thaliana DNA-binding sequencing experiments. Go to ReMap for more info.
ReMap 2022 Regulatory Atlas
ReMap 2022: A database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments Go to ReMap2022 for more info.
mm10, mm39, hg38, hg19, dm6, araTha1
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Couldn't open ftp://ftp.ebi.ac.uk/pub/databases/Rfam/12.0/genome_browser_hub/hub.txt Debug Help hg38, mm10, ce10, galGal4, ci2, danRer7, dm6, sacCer3
Roadmap Epigenomics Data Complete Collection at Wash U VizHub
Roadmap Epigenomics Human Epigenome Atlas Data Complete Collection, VizHub at Washington University in St. Louis
Roadmap Epigenomics Integrative Analysis Hub
Roadmap Epigenomics Integrative Analysis Hub at Washington University in St. Louis
Seq-data on mm9 NS5 cells
Set of sequencing data on mm9 NS5 cells
simplified human intestinal microbiota HUB
[+] bact, bifi, blautia, anaero, ery, clostri, lacto...
singing mouse genome hub
This is the genome hub for Alston's singing mouse (Scotinomys teguina).
Splice Site Usage Hub
Splice Site Usage Values Calculated for 19 ENCODE Cell Lines from RNA-seq
Synonymous Constraint Elements and Synonymous Acceleration Elements in protein-coding regions
hg19, hg38, wuhCor1
T cell ATACseq ChIPseq assembly by Pipkin lab
TOBIAS footprint prediction
Transcription factor Occupancy prediction By Investigation of ATAC-seq Signal
Translation Initiation Sites (TIS)
Translation Initiation Sites (TIS) track
UCD DNA methylation data
[+] hg19, hg18, mm10, mm9, bosTau7, bosTau6, canFam3...
UCSC Repeat Browser 2020 Update
Human Repeat consensuses annotated with lifted tracks
hg38reps, hg19, hg38
Ultra conserved Elements in the Human Genome. Science 304(5675) pp.1321-1325 (2004)
Umap and Bismap mappability
Uniquely mappable regions of genome and methylome
hg38, hg19, mm9, mm10
UMassMed H3K4me3 ChIP-seq data for Autistic brains
UniBind 2018 Hub
UniBind: A map of direct TF-DNA interactions from ChIP-seq and TF binding profiles
UniBind 2021 permissive Hub
UniBind 2021 hub for permissive direct TF-DNA interactions
[+] hg38, mm10, ce11, dm6, danRer11, spo2, sacCer3, rn6...
UniBind 2021 Robust Hub
UniBind 2021 hub for robust direct TF-DNA interactions
[+] hg38, mm10, ce11, dm6, danRer11, sacCer3, rn6, araTha1...
UniProtKB reviewed protein features mapped to the Ensembl genome assembly.
Vertebrate genome assemblies
[+] GCF_003597395.1, GCF_017654675.1...
Vertebrate Genomes Project primary assemblies
[+] GCA_009769605.1, GCA_009819775.1...
Viral genome assemblies
[+] GCF_000838645.1, GCF_000864245.1...
Vista Browser Track Hub
hg19, mm9, mm10
Wasp spider hub
This is the assembly hub of the wasp spider (Argiope bruennichi)
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Couldn't open ftp://ftp.wormbase.org/pub/wormbase/releases/current-production-release/MULTI_SPECIES/hub/hub.txt Debug Help
[+] brenneri, japonica, remanei, ovolvulus, briggsae...
Xiphophorus maculatus chromosome assembly version 5.0(SMRT)
Burgess Lab Zebrafish Genomic Resources
danRer11, danRer10, danRer7