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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RegulomeDB Resource Report Resource Website 100+ mentions |
RegulomeDB (RRID:SCR_017905) | data or information resource, service resource, database | Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature. | Annotate, SNP, regulatory, DNA, element, intergenic, region, human, genome, sequence, DNAase, hypersensitivity, binding, site, transcription, factor, promoter, region, data, FASEB list | NHGRI U54 HG 004558; Beta Cell Consortium |
PMID:22955989 | Free, Freely available | SCR_017905 | 2026-07-28 09:44:39 | 123 | |||||||||
|
ABA Mouse Brain: Atlas Resource Report Resource Website 100+ mentions |
ABA Mouse Brain: Atlas (RRID:SCR_017479) | data or information resource, service resource, database | Genome wide database of gene expression in mouse brain. Genome-wide atlas of gene expression in the adult mouse brain. | Genome, data, gene, expression, mouse, brain |
has parent organization: Allen Institute for Brain Science is provided by: Allen Brain Atlas |
PMID:17151600 | Free, Freely available | SCR_017479 | Allen Brain Atlas: Mouse Brain, , Allen Brain Atlas Mouse Brain: Atlas | 2026-07-28 09:44:34 | 328 | ||||||||
|
Molecular Signatures Database Resource Report Resource Website 500+ mentions |
Molecular Signatures Database (RRID:SCR_016863) | MSigDB | data or information resource, database | Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software. | collection, annotated, gene, set, GSEA, enrichment, analysis, genome, RNA, expression, data, FASEB list, DRKB |
uses: GSEA uses: Gene Set Enrichment Analysis has parent organization: Broad Institute |
NIH ; NIGMS ; NCI CA295532 |
Free, Freely available, Registration required to download GSEA software | https://www.gsea-msigdb.org/gsea/msigdb/ | SCR_016863 | Molecular Signatures Database, The Molecular Signatures Database, MSigDB, MSigDB database v6.2 | 2026-07-28 09:44:28 | 762 | ||||||
|
SVA Resource Report Resource Website 10+ mentions |
SVA (RRID:SCR_002155) | SVA | software application, commercial organization, software resource | Software package to annotate, visualize, and analyze the genetic variants identified through next-generation sequencing studies, including whole-genome sequencing (WGS) and exome sequencing studies. SVA aims to provide the research community with a user-friendly and efficient tool to analyze large amount of genetic variants, and to facilitate the identification of the genetic causes of human diseases and related traits. | gene, genetic, genomic, annotate, visualize, genetic variant, next-generation sequencing, whole-genome sequencing, exome, sequencing, genome, disease, trait, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Duke University School of Medicine; North Carolina; USA |
PMID:21624899 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154666, OMICS_00190, biotools:sequencevariantanalyzer | http://www.svaproject.org/, https://bio.tools/sequencevariantanalyzer | SCR_002155 | Sequence Variant Analyzer, SVA: Sequence Variant Analyzer | 2026-07-28 09:40:21 | 16 | |||||
|
Fast-SG Resource Report Resource Website 1+ mentions |
Fast-SG (RRID:SCR_015934) | software resource, algorithm resource | Algorithm for alignment-free scaffolding graph construction from short or long reads. It allows the reuse of efficient algorithms designed for short read data and permits the definition of novel modular hybrid assembly pipelines. | scaffolding, genome, assembly, illumina, nanopore, pacbio, hybrid, alignment, free, algorithm | CMM PFB03; CONICYT BECA DOCTORADO NACIONAL 21140124 |
DOI:10.1101/209122 | Open source, Free, Available for download, Runs on MAC OS, Runs on Linux | SCR_015934 | Fast SG | 2026-07-28 09:44:01 | 4 | ||||||||
|
DFCI Center for Cancer Computational Biology Resource Report Resource Website |
DFCI Center for Cancer Computational Biology (RRID:SCR_012688) | DFCI CCCB | access service resource, service resource, core facility | Core facility that provides the following services: Microarray and other genomic data analysis, MiSeq. The Center provides broad-based support for the generation, analysis, and interpretation of genomic and other large-scale data in the context of basic, clinical and translational research. The CCCB has three primary elements. * The CCCB sequencing facility offers a wide range of services to assist in the design and execution of next-generation sequencing projects. Utilizing the Illumina (Solexa) sequencing technology, they currently support a number of applications inlcuding ChIP-Seq, RNA-Seq, whole genome, whole exome, and targeted re-sequencing. * The analytical services and support platform aims to provide state-of-the-art assistance in the collection, management, analysis, and interpretation of large-scale data with a focus on data generated using ''''omic technologies. In addition, they offer software, services, and training designed to assist investigators in advancing their research. * The CCCB research program is focused on development of new methods for improving analysis and interpretation of genomic data through integration of diverse data types with the goal of creating open-source software tools to be made freely-available to the research community. | nucleic acid microarray assay, next generation sequencing, genome, genomic, microarray |
is listed by: ScienceExchange is listed by: Eagle I is related to: Dana-Farber Cancer Institute Labs and Facilities has parent organization: Dana-Farber Cancer Institute |
Cancer | SciEx_8878 | http://harvard.eagle-i.net/i/0000012e-59a5-5f86-55da-381e80000000, http://www.scienceexchange.com/facilities/center-for-cancer-computational-biology-cccb-harvard | SCR_012688 | Dana-Farber Cancer Institute Center for Cancer Computational Biology, DFCI Center for Cancer Computational Biology (CCCB) | 2026-07-28 09:43:15 | 0 | ||||||
|
Stanford University School of Medicine High Throughput Bioscience Center Core Facility Resource Report Resource Website 1+ mentions |
Stanford University School of Medicine High Throughput Bioscience Center Core Facility (RRID:SCR_017794) | HTBC | access service resource, service resource, core facility | Core provides fully automated high throughput screening (HTS) of Compound Libraries (130,000+ compounds) for both enzyme/protein-based assays and cell-based assays, using Caliper Life Sciences Staccato system;Genomic siRNA screening with siARRAY whole human genome siRNA library from Dharmacon targeting 21,000 genes, using Agilent Bravo system;High-Content Screening using ImageXpress Micro automated fluorescent microscope with live cell, bright field, phase contrast and integrated plate handling with Thermo Catalyst CRS, and image analysis using MetaXpress software;High Throughput Molecular Biology reagents and services, including access to cDNA libraries (Human ORFeome collection, 15,000 genes) and 96 and 384-well bead clean-ups and PCR setup (Biomek FX and Agilent Bravo), and other automation steps in collaboration with SFGF;High-throughput assay development assistance with cell culture, experiment design, robotic programming and Standard Operating Procedure drafting;Screening data analysis assistance with protocols, hit determination and structure activity analyses using MDL chemical database ISIS/HOST, Plate Manager, Assay Explorer and Report Manager. Use of microplate reader detection systems, including Tecan Infinite M1000 and Infinite M1000 PRO and Molecular Devices Analyst GT for fluorescence; fluorescence polarization; time-resolved fluorescence; absorbance and luminescence (with injectors and AlphaScreen); and Flexstation II 384, for kinetic fluorescence reads to measure calcium mobilization and ion channels.Use of liquid-handling robots, including Sciclone ALH3000 (96- and 384-well pipetting), Agilent Bravo (96- and 384-well pipetting), Velocity11 VPrep (96-well pipetting), Bio-Tek plate washers/dispensers, Matrix Wellmate and Titertek/Labsystems Multidrop microplate dispensers, and Velocity11 PlateLoc plate heat sealer;Training for most of these services. | High, throughput, bioscience, automated, screening, compound, library, enzyme, protein, assay, human, whole, genome, cDNA, service, core | Open | SCR_023235, ABRF_2460 | https://coremarketplace.org/?FacilityID=2460 | SCR_017794 | High Throughput Bioscience Center | 2026-07-28 09:44:33 | 1 | |||||||
|
University of California-Davis Mouse Biology Program CRISPR Based Genome Editing Service Core Facility Resource Report Resource Website 1+ mentions |
University of California-Davis Mouse Biology Program CRISPR Based Genome Editing Service Core Facility (RRID:SCR_017851) | MBP | access service resource, service resource, core facility | Core located on campus of UC Davis, providing fully customized support for scientific research using genetically altered mice. Provides access to develop, plan, execute, and analyze research project involving genetically-altered mice. Provides description of project, including alternative approaches, accurate timelines, and cost estimates.Provides regular and informative communication throughout project, including email updates on completion of each milestone. Project progress can be followed at each stage by viewing detailed information anytime by accessing our online and secure project tracking system (PTS) available 24 hours a day. | Mouse, CRISPR, genome, editing, project, develop, plan, execute, analyze, genetically, altered, service, core, ABRF | is listed by: ABRF CoreMarketplace | Open | ABRF_660 | SCR_017851 | UC Davis Mouse Biology Program | 2026-07-28 09:44:44 | 8 | |||||||
|
Albert Einstein College of Medicine Molecular Cytogenetics Core Facility Resource Report Resource Website |
Albert Einstein College of Medicine Molecular Cytogenetics Core Facility (RRID:SCR_017815) | MC | access service resource, service resource, core facility | Core provides tools for preparation of human and murine samples suitable for molecular genetic and cytogenetic analysis of entire genome. These tools include establishment of EBV transformed cell lines; isolation of DNA and mRNA from variety of tissue culture samples as well as primary biopsies; preparation of metaphase chromosomes suitable for fluorescence in situ hybridization (FISH) and Spectral Karyotyping (SKY) or whole chromosome paints for human and mouse genome. Core personnel is trained to hybridize commercial probes and to designed locus specific probes for regions of interest to investigators. All probes are custom designed and in house generated. | Molecular, cytogenetic, preparation, human, murine, sample, genetic, analysis, genome, DNA, mRNA, isolation, metaphase, chromosome, fluorescence, in situ, hybridization, spectra, kayotyping, commercial, design, locus, specific, probe, service, core, ABRF | is listed by: ABRF CoreMarketplace | Open | ABRF_580 | SCR_017815 | Molecular Cytogenetics Core Albert Einstein College of Medicine | 2026-07-28 09:44:34 | 0 | |||||||
|
University of Miami Miller School of Medicine Gene Expression Core Facility Resource Report Resource Website |
University of Miami Miller School of Medicine Gene Expression Core Facility (RRID:SCR_017825) | access service resource, service resource, core facility | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 27,2025. CGT gene expression core utilizes Affymetrix GeneChip Arrays and Illumina BeadChips to identify gene expression variation in single genes, targeted set of genes, or entire genomes. Affymetrix GeneChip Arrays Human Gene ST,Human Transcriptome Array 2.0, Human Exon ST, Human miRNA, Illumina Expression, HumanHT-12 v4 BeadChip. | Gene, expression, genome, identify, human, Affymetrix, GeneChip, Array, Illumina, BeadChip, service, core, ABRF |
is listed by: ABRF CoreMarketplace has parent organization: University of Miami Miller School of Medicine; Florida; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | ABRF_598 | https://coremarketplace.org/?FacilityID=598&citation=1 | SCR_017825 | Gene Expression at the CGT | 2026-07-28 09:44:38 | 0 | |||||||
|
New York University School of Medicine Langone Health Genome Technology Center Core Facility Resource Report Resource Website 50+ mentions |
New York University School of Medicine Langone Health Genome Technology Center Core Facility (RRID:SCR_017929) | NYU GTC, GTC | access service resource, service resource, core facility | Core provides range of services related to genome, epigenome, and transcriptome analysis. Offers technologies including Illumina deep sequencing and sample preparation for variety of applications, including DNA and RNA sequencing (DNA- and RNA-seq), exome sequencing, targeted capture, chromatin immunoprecipitation sequencing (ChIP-seq), methylation sequencing (Methyl-seq), metagenomics, and many others;Automation of Illumina library and targeted capture preps, including 16S ribosomal RNA (rRNA) sequencing;Oxford Nanopore sequencing (long reads);Bio-Rad Droplet Digita polymerase chain reaction (PCR);Nanostring nCounter;Single-cell RNA- and DNA-seq using the C1 Auto Prep System from Fluidigm, and 10x Genomics Chromium System.Provides expertise on strategies to achieve research goals in any field related to genomics, and can tailor bioinformatics analysis to individual project. If you supply us with nucleic acids, we can perform every step required to help you achieve your desired results. | Genome, epigenome, transcriptome, analysis, deep, sequencing, sample, preparation, DNA, RNA, exome, rRNA, genomics, analysis, service, core, ABRF, USEDit |
is listed by: ABRF CoreMarketplace is listed by: ScienceExchange is related to: USEDit has parent organization: New York University School of Medicine; New York; USA |
NIH Office of the Director S10 OD023423 | Open | ABRF_824, SciEx_41, SCR_012514 | https://coremarketplace.org/?FacilityID=824&citation=1 | http://www.scienceexchange.com/facilities/genome-technology-center-nyu | SCR_017929 | NYU Langone's Genome Technology Center, New York University School of Medicine Genome Technology Center, New York University School of Medicine Langone Health Genome Technology Center | 2026-07-28 09:44:36 | 72 | ||||
|
Johns Hopkins University School of Medicine Genetic Resources Core Facility Resource Report Resource Website 50+ mentions |
Johns Hopkins University School of Medicine Genetic Resources Core Facility (RRID:SCR_018669) | GRCF | access service resource, service resource, core facility | Established to produce immortalized cell lines from human blood (EBV transformations). Offers genomics applications for single cells, including RNA-seq, gene expression profiling by qPCR and DNA amplification for whole-genome or targeted (exome or PCR-based analysis) through 10x Genomics Chromium platform (similar to Drop Seq). Offers custom genotyping to analyze short tandem repeats, variable number tandem repeats and single nucleotide polymorphisms. | USEDit, immortalized cell line production, human blood, RNAseq, gene expression profiling, qPCR, DNA amplification, exome, genome, PCR, analysis, ABRF |
is listed by: ABRF CoreMarketplace is related to: USEDit has parent organization: Johns Hopkins University; Maryland; USA |
ABRF_344 | https://grcf.jhmi.edu/grcf-services/ | https://grcf.jhmi.edu/biorepository-cell-center/ | SCR_018669 | GRCF Cell Center, Genetic Resources Core Facility, JHU-NAT, GRCF Biorepository and Cell Center, GRCF DNA Services, Genetic Resources Core Facility (GRCF) BioRepository and Cell Center, JHU Nucleic Acid Technologies, JHU BioBank | 2026-07-28 09:44:43 | 52 | ||||||
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Albert Einstein College of Medicine Epigenomics Shared Core Facility Resource Report Resource Website 1+ mentions |
Albert Einstein College of Medicine Epigenomics Shared Core Facility (RRID:SCR_023284) | ESF | access service resource, service resource, core facility | Part of Einstein Center for Epigenomics and Illumina CSPro (certified service provider) laboratory, offers massively-parallel sequencing (MPS) including fully-automated library preparation, quality control and assurance, and number of assays to study the genome/epigenome. Data analytical services are provided by Computational Genomics Facility. | USEDit, ABRF, massively-parallel sequencing, fully automated library preparation, quality control and assurance, genome, epigenome, data analytical services, |
is listed by: ABRF CoreMarketplace has parent organization: Albert Einstein College of Medicine; New York; USA |
ABRF_1686 | https://coremarketplace.org/?FacilityID=1686&citation=1 | https://www.einsteinmed.edu/research/shared-facilities/cores/53/epigenomics/ | SCR_023284 | Albert Einstein College of Medicine Epigenomics Shared Facility (ESF), Epigenomics Shared Facility (ESF) | 2026-07-28 09:45:54 | 2 | ||||||
|
compleasm Resource Report Resource Website 1+ mentions |
compleasm (RRID:SCR_026370) | source code, software resource | Software genome completeness evaluation tool based on miniprot. | genome completeness evaluation, genome, completeness evaluation, | NHGRI R01HG010040; Chan-Zuckerberg Initiative |
PMID:37758247 | Free, Available for download, Freely available | SCR_026370 | 2026-07-28 09:46:38 | 8 | |||||||||
|
BVSim Resource Report Resource Website 1+ mentions |
BVSim (RRID:SCR_026926) | BVSim | software application, software resource, software development tool, code profiler, simulation software | Software package provides several functions and parameters for simulating genetic variations. Benchmarking variation simulator mimicking human variation spectrum. | genome, structural alteration, simulating genetic variations, | Free, Available for download, Freely available | SCR_026926 | Benchmarking Variation Simulator | 2026-07-28 09:46:53 | 1 | |||||||||
|
SlideTags.wdl Resource Report Resource Website |
SlideTags.wdl (RRID:SCR_027567) | software application, software resource, data analysis software, data processing software | Software pipeline as open-source, cloud-optimized workflow for processing spatial transcriptomics data. It supports data derived from spatially barcoded sequencing technologies, including Slide-tags-based single-molecule profiling. The pipeline processes raw sequencing data into spatially resolved gene expression matrices, ensuring accurate alignment, spatial positioning, and quantification. | Spatial transcriptomics data, single-cell data, Slide-tags technology data, spatial barcode processing pipeline, spatial gene expression quantification, reads alignment, genome, spatial positioning, human tissue data analysis, 5 alpha-SR2 |
has parent organization: Broad Institute is organization facet of: BRAIN Initiative Cell Atlas Network |
Free, Available for download, Freely available | SCR_027567 | Slide-tags | 2026-07-28 09:47:12 | 0 |
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