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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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RecountDB Resource Report Resource Website |
RecountDB (RRID:SCR_006117) | RecountDB | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database for corrected read counts and genome mapping on NCBI's Short Read Archive. The corrected count was done using RECOUNT and the mapping with LAST. We also provide information of reference genome to which we aligned the short reads. We focus on transcriptomic data, specifically TSS-Seq and RNA-Seq. Because this is the type of data for which sequence count correction is most important. Hence we do not include the genomic reads. The current version contains 2,265 entries from 45 organisms, with read lengths from 17 to 100bp. Via a searchable and browseable interface users can obtain corrected data in formats useful for transcriptomic analysis. We provide the data grouped according to the genome, type of studies and submitter in TAB , PSL and BAM format. They contain the mapping position and annotation of reads observed and corrected counts. | read count, genome mapping, short read, genome, transcript, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: NCBI Sequence Read Archive (SRA) is related to: RECOUNT is related to: LAST has parent organization: National Institute of Advanced Industrial Science and Technology |
Japanese Ministry of Education Culture Sports Science and Technology MEXT 221S002 | PMID:22139942 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_151592, biotools:recountdb | https://bio.tools/recountdb | SCR_006117 | 2026-09-19 12:56:56 | 0 | |||||
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ProOpDB Resource Report Resource Website 10+ mentions |
ProOpDB (RRID:SCR_006111) | ProOpDB | data or information resource, database | The Prokaryotic Operon DataBase (ProOpDB) constitutes one of the most precise and complete repository of operon predictions in our days. Using our novel and highly accurate operon algorithm, we have predicted the operon structures of more than 1,200 prokaryotic genomes. ProOpDB offers diverse alternatives by which a set of operon predictions can be retrieved including: i) organism name, ii) metabolic pathways, as defined by the KEGG database, iii) gene orthology, as defined by the COG database, iv) conserved protein motifs, as defined by the Pfam database, v) reference gene, vi) reference operon, among others. In order to limit the operon output to non-redundant organisms, ProOpDB offers an efficient protocol to select the more representative organisms based on a precompiled phylogenetic distances matrix. In addition, the ProOpDB operon predictions are used directly as the input data of our Gene Context Tool (GeConT) to visualize their genomic context and retrieve the sequence of their corresponding 5�� regulatory regions, as well as the nucleotide or amino acid sequences of their genes. The prediction algorithm The algorithm is a multilayer perceptron neural network (MLP) classifier, that used as input the intergenic distances of contiguous genes and the functional relationship scores of the STRING database between the different groups of orthologous proteins, as defined in the COG database. Nevertheless, the operon prediction of our method is not restricted to only those genes with a COG assignation, since we successfully defined new groups of orthologous genes and obtained, by extrapolation, a set of equivalent STRING-like scores based on conserved gene pairs on different genomes. Since the STRING functional relationships scores are determined in an un-bias manner and efficiently integrates a large amount of information coming from different sources and kind of evidences, the prediction made by our MLP are considerably less influenced by the bias imposed in the training procedure using one specific organism. | genome, operon, gene pair, gene, operon prediction, metabolic pathway, gene orthology, conserved protein motif, protein motif, reference gene, reference operon, visualization, regulatory region, nucleotide, amino acid, sequence, phylogeny, FASEB list |
is related to: COG is related to: KEGG is related to: Pfam has parent organization: National Autonomous University of Mexico; Mexico City; Mexico |
CONACyT 60127-Q; CONACyT SALUD-2007-C01-68992; DGAPA IN212708 |
PMID:20385580 | nlx_151585 | SCR_006111 | Prokaryotic Operon DataBase (ProOpDB), Prokaryotic Operon DataBase | 2026-09-19 12:56:56 | 35 | ||||||
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Tuberculosis Database Resource Report Resource Website 50+ mentions |
Tuberculosis Database (RRID:SCR_006619) | TBDB | data or information resource, database | Database providing integrated access to genome sequence, expression data and literature curation for Tuberculosis (TB) that houses genome assemblies for numerous strains of Mycobacterium tuberculosis (MTB) as well assemblies for over 20 strains related to MTB and useful for comparative analysis. TBDB stores pre- and post-publication gene-expression data from M. tuberculosis and its close relatives, including over 3000 MTB microarrays, 95 RT-PCR datasets, 2700 microarrays for human and mouse TB related experiments, and 260 arrays for Streptomyces coelicolor. (July 2010) To enable wide use of these data, TBDB provides a suite of tools for searching, browsing, analyzing, and downloading the data. | genomic, protein, blast, genome, gene, systems biology, gene expression, microarray, comparative analysis, regulatory network, metabolic network, epitope, expression profile, rt-pcr, gene regulation, genome browser, FASEB list |
is listed by: re3data.org is related to: SMD is related to: BioCyc has parent organization: Broad Institute has parent organization: Stanford University School of Medicine; California; USA |
Tuberculosis | Bill and Melinda Gates Foundation | PMID:20488753 PMID:18835847 |
Acknowledgement requested, Public, (Published data) | nif-0000-03537, r3d100010930 | https://doi.org/10.17616/R39G8F | SCR_006619 | TB Database, TBDatabase | 2026-09-19 12:56:59 | 64 | |||
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DBM-DB Resource Report Resource Website 10+ mentions |
DBM-DB (RRID:SCR_006258) | DBM-DB | data or information resource, database | Database storing and integrating genomic data of diamondback moth (DBM), Plutella xylostella (L.). It provides comprehensive search tools and downloadable datasets for scientists to study comparative genomics, biological interpretation and gene annotation of this insect pest. DBM-DB contains assembled transcriptome datasets from multiple DBM strains and developmental stages, and the annotated genome of P. xylostella (version 2). They have also integrated publically available ESTs from NCBI and a putative gene set from a second DBM genome (KONAGbase) to enable users to compare different gene models. DBM-DB was developed with the capacity to incorporate future data resources, and will serve as a long-term and open-access database that can be conveniently used for research on the biology, distribution and evolution of DBM. This resource aims to help reduce the impact DBM has on agriculture using genomic and molecular tools. | genome, rna-seq, gene expression profiling, micrornas, metagenomics, blast, gbrowse, FASEB list |
is listed by: OMICtools has parent organization: Fujian Agriculture and Forestry University; Fujian; China |
PMID:24434032 | Free, Public | OMICS_02235 | http://59.79.254.1/DBM/ | SCR_006258 | Diamondback moth Genome Database | 2026-09-19 12:56:57 | 32 | |||||
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ViralZone Resource Report Resource Website 100+ mentions |
ViralZone (RRID:SCR_006563) | ViralZone | data or information resource, database | ViralZone is a SIB Swiss Institute of Bioinformatics web-resource for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries. ViralZone project is handled by the virus program of SwissProt group. Proteins popups were developed in collaboration with Prof. Christian von Mering and Andrea Franceschini, Bioinformatics Group , Institute of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland, funded in part by the SIB Swiss Institute of bioinformatics. All pictures in ViralZone are copyright of the SIB Swiss Institute of Bioinformatics. | dna virus, rna virus, virus, dna, rna, genomic, proteomic, sequence, reference strain, image, virion, retro-transcribing virus, genome, bibliographic, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: SIB Swiss Institute of Bioinformatics |
Swiss Institute of Bioinformatics | PMID:20947564 | biotools:viralzone, r3d100013314, nlx_144372 | https://bio.tools/viralzone, https://doi.org/10.17616/R31NJMRM | http://www.expasy.org/viralzone/ | SCR_006563 | Viral Zone | 2026-09-19 12:56:59 | 148 | ||||
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DFCI Center for Cancer Computational Biology Resource Report Resource Website |
DFCI Center for Cancer Computational Biology (RRID:SCR_012688) | DFCI CCCB | access service resource, core facility, service resource | 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) | 2026-09-19 12:59:13 | 0 | ||||||
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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, core facility, service resource | 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 | 2026-09-19 12:59:31 | 0 | |||||||
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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, core facility, service resource | 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 | 2026-09-19 12:59:31 | 0 | |||||||
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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, core facility, service resource | 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 | 2026-09-19 12:59:30 | 1 | |||||||
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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, core facility, service resource | 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 | 2026-09-19 12:59:34 | 90 | ||||
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University of California-Davis Mouse Biology Program CRISPR Based Genome Editing Service Core Facility Resource Report Resource Website 10+ mentions |
University of California-Davis Mouse Biology Program CRISPR Based Genome Editing Service Core Facility (RRID:SCR_017851) | MBP | access service resource, core facility, service resource | 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 | 2026-09-19 12:59:32 | 10 | |||||||
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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, core facility, service resource | 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 | 2026-09-19 12:59:36 | 60 | ||||||
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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, core facility, service resource | 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) | 2026-09-19 12:59:55 | 5 | ||||||
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compleasm Resource Report Resource Website 10+ mentions |
compleasm (RRID:SCR_026370) | software resource, source code | Software genome completeness evaluation tool based on miniprot. | genome completeness evaluation, genome, completeness evaluation, | Chan-Zuckerberg Initiative ; NHGRI R01HG010040 |
PMID:37758247 | Free, Available for download, Freely available | SCR_026370 | 2026-09-19 01:00:47 | 10 | |||||||||
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BVSim Resource Report Resource Website 1+ mentions |
BVSim (RRID:SCR_026926) | BVSim | code profiler, simulation software, software application, software development tool, software resource | 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 | 2026-09-19 01:01:01 | 1 | |||||||||
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SlideTags.wdl Resource Report Resource Website 1+ mentions |
SlideTags.wdl (RRID:SCR_027567) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-19 01:01:13 | 2 |
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