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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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BlobTools2 Resource Report Resource Website 100+ mentions |
BlobTools2 (RRID:SCR_023351) | software resource, data processing software, software application, data analysis software | Software suite for identifying and isolating non-target data in draft and publicly available genome assemblies. Used to process assembly, read and analysis files for fully reproducible interactive exploration in browser-based Viewer. Used for interactive quality assessment of genome assemblies .BlobTools2 is reimplementation of BlobTools, written in Python 3 with fully modular design to make creating new datasets and adding additional analysis types easier. | interactive quality assessment, genome assemblies, identifying and isolating non-target data, genome, QC, filtering, process assembly, read and analysis files, |
is related to: Blobtools is related to: Blobtoolkit |
BBSRC Bioinformatics and Biological Resources fund | PMID:32071071 | Free, Available for download, Freely available | https://github.com/blobtoolkit/blobtoolkit | SCR_023351 | blobtoolkit | 2026-08-03 09:37:59 | 382 | ||||||
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CRISPOR Resource Report Resource Website 1000+ mentions |
CRISPOR (RRID:SCR_015935) | software resource, web application | Web application that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. This sgRNA design tool assists with guide selection in a variety of genomes and pre-calculated results for all human coding exons as a UCSC Genome Browser track. | rna, sg, sgrna, crispr, genome, off-target, prediction, accuracy, clone, cas9, coding, exon | is related to: UCSC Genome Browser | MRC 53658; NIH Office of the Director U42 OD011174; NHGRI U41 HG002371; NCI U54 HG007990; California Institute of Regenerative Medicine GC1R-06673C; Agence Nationale pour la Recherche ; Fondation pour la Recherche Médicale DEQ20140329544 |
PMID:27380939 | Free, Available for download | https://github.com/maximilianh/crisporWebsite | SCR_015935 | 2026-08-03 09:36:30 | 1320 | |||||||
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loadBAM2ge_db Resource Report Resource Website 1+ mentions |
loadBAM2ge_db (RRID:SCR_015951) | software resource, data visualization software, software application, data processing software | Software pipeline that visualizes mapping results (in BAM format) on Genome Explorer. | bam, map, mapping, genome, pipeline, maser, visualization, explorer | Public | SCR_015951 | loadBAM2ge_db (PE) | 2026-08-03 09:36:15 | 1 | ||||||||||
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GRS Resource Report Resource Website 1+ mentions |
GRS (RRID:SCR_001008) | data management software, software application, data processing software, data analysis software, software resource | A compression tool for efficient storage of Genome Re-Sequencing data. GRS processes genome sequence data without use of reference SNPs and other variants. It can also automatically rebuild the individual genome sequence data using the reference genome sequence. | data analysis software, data management software, compression tool, data compression, storage, genome, resequencing | is listed by: OMICtools | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00960 | SCR_001008 | 2026-08-03 09:31:13 | 2 | |||||||||
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NTAP Resource Report Resource Website 10+ mentions |
NTAP (RRID:SCR_001488) | NTAP | software resource, data processing software, software application, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software for tiling array data analysis to survey the genome-wide binding sites of transcription factor HY5 in Arabidopsis and the genome-wide histone modifications/DNA methylation level in rice. It was developed in the process of generating NimbleGen analysis. Written in R and Perl. | software, tiling array, data analysis, rice, arabidopsis, hy5, transcription factor, genome |
is listed by: OMICtools has parent organization: Peking University; Beijing; China |
PMID:19468055 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00808 | SCR_001488 | NimbleGen Tiling array Analysis Package, NimbleGen Tilingarray Analysis Package | 2026-08-03 09:31:20 | 10 | ||||||
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Pathosystems Resource Integration Center Resource Report Resource Website 1000+ mentions |
Pathosystems Resource Integration Center (RRID:SCR_004154) | PATRIC | production service resource, data analysis service, service resource, bioinformatics resource center, database, analysis service resource, data or information resource | A Bioinformatics Resource Center bacterial bioinformatics database and analysis resource that provides researchers with an online resource that stores and integrates a variety of data types (e.g. genomics, transcriptomics, protein-protein interactions (PPIs), three-dimensional protein structures and sequence typing data) and associated metadata. Datatypes are summarized for individual genomes and across taxonomic levels. All genomes, currently more than 10 000, are consistently annotated using RAST, the Rapid Annotations using Subsystems Technology. Summaries of different data types are also provided for individual genes, where comparisons of different annotations are available, and also include available transcriptomic data. PATRIC provides a variety of ways for researchers to find data of interest and a private workspace where they can store both genomic and gene associations, and their own private data. Both private and public data can be analyzed together using a suite of tools to perform comparative genomic or transcriptomic analysis. PATRIC also includes integrated information related to disease and PPIs. The PATRIC project includes three primary collaborators: the University of Chicago, the University of Manchester, and New City Media. The University of Chicago is providing genome annotations and a PATRIC end-user genome annotation service using their Rapid Annotation using Subsystem Technology (RAST) system. The National Centre for Text Mining (NaCTeM) at the University of Manchester is providing literature-based text mining capability and service. New City Media is providing assistance in website interface development. An FTP server and download tool are available. | genomics, genome, transcriptomics, protein-protein interaction, sequence typing, proteobacteria, brucella, rickettsia, coxiella, coronavirus, calicivirus, lyssavirus, virus, hepatitis a, hepatitis e, pathway, proteome, metabolic pathway, drug, vaccine, diagnostics, FASEB list |
is listed by: OMICtools has parent organization: Virginia Polytechnic Institute and State University; Virginia; USA |
NIAID | PMID:24225323 PMID:17142235 |
Free, Public, Acknowledgement requested | r3d100010142, OMICS_01658, nlx_17476 | http://patricbrc.vbi.vt.edu/portal/portal/patric/Home, https://doi.org/10.17616/R3WS3X | http://patric.vbi.vt.edu/ | SCR_004154 | PathoSystems Resource Integration Center, PATRIC, Pathosystems Resource Integration Center | 2026-08-03 09:32:37 | 1083 | |||
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Gene Weaver Resource Report Resource Website 10+ mentions |
Gene Weaver (RRID:SCR_003009) | data repository, production service resource, data analysis service, service resource, database, storage service resource, analysis service resource, data or information resource | Freely accessible phenotype-centered database with integrated analysis and visualization tools. It combines diverse data sets from multiple species and experiment types, and allows data sharing across collaborative groups or to public users. It was conceived of as a tool for the integration of biological functions based on the molecular processes that subserved them. From these data, an empirically derived ontology may one day be inferred. Users have found the system valuable for a wide range of applications in the arena of functional genomic data integration. | phenotype, microarray, gene, genome, functional genomics, process, pathway, function, gene set, genomic data integration, analysis, visualization |
is used by: NIF Data Federation is used by: Integrated Datasets is listed by: OMICtools is related to: Integrated Manually Extracted Annotation has parent organization: Jackson Laboratory |
Integrative Neuroscience Initiative on Alcoholism ; NIAAA U01 AA13499; NIAAA U24 AA13513; NIAAA R01 AA18776 |
PMID:22080549 PMID:19733230 |
Free, Freely available | r3d100012464, OMICS_02232, nif-0000-00517 | http://ontologicaldiscovery.org/, https://doi.org/10.17616/R3248T | SCR_003009 | GeneWeaver, GeneWeaver - A system for the integration of functional genomics experiments, Ontological Discovery Environment, GeneWeaver.org | 2026-08-03 09:31:55 | 34 | |||||
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Sequence Tag Alignment and Consensus Knowledgebase Database Resource Report Resource Website |
Sequence Tag Alignment and Consensus Knowledgebase Database (RRID:SCR_002156) | database, software application, data processing software, data or information resource, software resource, data visualization software | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The STACKdb is knowledgebase generated by processing EST and mRNA sequences obtained from GenBank through a pipeline consisting of masking, clustering, alignment and variation analysis steps. The STACK project aims to generate a comprehensive representation of the sequence of each of the expressed genes in the human genome by extensive processing of gene fragments to make accurate alignments, highlight diversity and provide a carefully joined set of consensus sequences for each gene. The STACK project is comprised of the STACKdb human gene index, a database of virtual human transcripts, as well as stackPACK, the tools used to create the database. STACKdb is organized into 15 tissue-based categories and one disease category. STACK is a tool for detection and visualization of expressed transcript variation in the context of developmental and pathological states. The data system organizes and reconstructs human transcripts from available public data in the context of expression state. The expression state of a transcript can include developmental state, pathological association, site of expression and isoform of expressed transcript. STACK consensus transcripts are reconstructed from clusters that capture and reflect the growing evidence of transcript diversity. The comprehensive capture of transcript variants is achieved by the use of a novel clustering approach that is tolerant of sub-sequence diversity and does not rely on pairwise alignment. This is in contrast with other gene indexing projects. STACK is generated at least four times a year and represents the exhaustive processing of all publicly available human EST data extracted from GenBank. This processed information can be explored through 15 tissue-specific categories, a disease-related category and a whole-body index | exonic, expressed, expressed sequence tag (est), expression, fragment, gene, alignment, alternative gene, cdna, clone, cluster, developmental, disease, diversity, genome, homo sapiens, human, isoform, knowledgebase, meta-cluster, mrna, pathological, sequence, tissue, transcript, variant, visualization | PMID:11125101 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20946 | SCR_002156 | STACKdb | 2026-08-03 09:31:46 | 0 | ||||||||
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UK Sheep Genome Mapping Project Resource Report Resource Website 1+ mentions |
UK Sheep Genome Mapping Project (RRID:SCR_002272) | topical portal, data or information resource, database, portal | THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The project aims to apply genome mapping research to sheep, utilizing previous research in sheep (in other countries) and in other species (in the UK and abroad) to the benefit of the UK sheep industry. The project itself uses existing breeding structures, knowledge of the sheep genome and experimental resources. It has three main aims: i) To use the Suffolk, Texel and Charollais Sire Referencing Schemes to detect and verify quantitative trait loci (QTLs) for growth and carcass composition traits ii) To investigate candidate genes and/or chromosomal regions for associations with production traits. iii) To investigate approaches for optimizing future genotyping strategies within the sire referencing schemes for practical and cost effective application of marker-assisted selection By using commercial breeding populations for the research, immediate application of beneficial results is possible. Potential benefits include increased genetic progress through marker assisted selection which utilizes the genotype information, correction of possible parentage errors (ultimately leading to additional genetic progress) and opportunities for using marker information for product certification. The project will benefit the UK sheep industry by the use of Marker Assisted Selection (MAS) utilizing QTL or gene variants identified in the project. Additional benefits may arise from parentage verification and correction of errors e.g. misallocation of lamb to ewe. In the longer term, opportunities may exist to use markers for quality control, tracing products to their source. The major advantage of the design of this project is that the results are immediately applicable to the breeding schemes within which the QTLs and/or genes are detected. The time lag in the application of the results that is often seen with experimental populations is minimized. The project requires close involvement with the Sire Reference Schemes, in return for their assistance the results have immediate benefit to animals within these groups. | gene, animal, breed, breeding, chromosomal, chromosome, genome, genotype, genotyping, lamb, map, mapping, marker, population, production, region, sheep, specie, structure, trait | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-20995 | SCR_002272 | UKSGMP | 2026-08-03 09:31:44 | 1 | |||||||||
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Codon Usage Analyzer Resource Report Resource Website |
Codon Usage Analyzer (RRID:SCR_018500) | Bio::CUA, Bio-CUA | software resource, data processing software, software application, data analysis software | Software tool as flexible and comprehensive codon usage analyzer. Used to analyze codon usage bias (CUB) and relevant problems. | Codon usage analyzer, codon, codon usage bias, genome, gene, codon, sequence | has parent organization: University of Rochester; New York; USA | David and Lucile Packard Foundation ; University of Rochester |
DOI:10.1101/022814 | Free, Freely available | https://metacpan.org/release/Bio-CUA | SCR_018500 | 2026-08-03 09:36:58 | 0 | ||||||
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rVista Resource Report Resource Website 10+ mentions |
rVista (RRID:SCR_018707) | production service resource, web service, analysis service resource, data access protocol, service resource, software resource | Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites. | Noncoding sequence, regulatory potential analysis, matrices search, TRANSFAC library collection, cis regulatory element, process alignment, zPicture, blastz, pairwise alignment, genome, analysis, transcription factor binding site, bio.tools |
is listed by: Debian is listed by: bio.tools works with: TRANSFAC |
PMID:15215384 | Free, Freely available | biotools:rvista | https://bio.tools/rvista | SCR_018707 | rVista 2.0 | 2026-08-03 09:37:04 | 30 | ||||||
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FunCoup Resource Report Resource Website 1+ mentions |
FunCoup (RRID:SCR_018711) | web service, database, service resource, data access protocol, data or information resource, software resource | Database of genome wide functional coupling networks. Provides tools to explore predicted networks and to retrieve detailed information about data underlying each prediction. Web service for functional coupling search. | Genome, genome functional coupling network, coupling network, functional coupling, functional couplings search, gene identifier, genome data | has parent organization: Karolinska Institute; Stockholm; Sweden | Swedish Research Council ; Stockholm University |
PMID:24185702 | Free, Freely available | SCR_018711 | 2026-08-03 09:37:04 | 3 | ||||||||
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Preseq Resource Report Resource Website 10+ mentions |
Preseq (RRID:SCR_018664) | software toolkit, software application, data processing software, data analysis software, software resource | Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries. | Genome, high throughput sequencing, predicting library complexity, distinct yield prediction, genomic library, initial sequencing experiment, molecular complexity prediction, sequencing libraryb, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Stanford University; Stanford; California |
PMID:23435259 | Free, Freely available | biotools:preseq | https://github.com/smithlabcode/preseq, https://bio.tools/preseq | SCR_018664 | 2026-08-03 09:37:04 | 19 | |||||||
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Differential Methylation Analysis Package Resource Report Resource Website |
Differential Methylation Analysis Package (RRID:SCR_019148) | DMAP | software toolkit, software application, data processing software, data analysis software, software resource | Software package for large scale genomic DNA methylation analysis. Filters and processes aligned bisulphite sequenced data to generate comprehensive reference methylomes in different units for any genome. Processes aligned SAM files of multiple samples to provide reliable and statistically significant differentially methylated regions, then relate them to proximal genes and CpG features with reasonable rapidity. | Genomic DNA methylation, DNA methylation analysis, bisulphite sequenced data, reference methylomes generation, genome, aligned SAM files processing, differentially methylated regions | has parent organization: University of Otago; Dunedin; New Zealand | National Centre for Growth and Development and Health Research Council ; New Zealand |
PMID:24608764 | Free, Freely available | SCR_019148 | 2026-08-03 09:37:11 | 0 | |||||||
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EnteroBase Resource Report Resource Website 100+ mentions |
EnteroBase (RRID:SCR_019019) | web service, database, data access protocol, data or information resource, software resource | Integrated software environment that supports identification of global population structures within several bacterial genera that include pathogens. Web service for analyzing and visualizing genomic variation within bacteria. Genome database to enable to identify, analyse, quantify and visualise genomic variation within bacterial genera including Salmonella, Escherichia/Shigella, Clostridioides,Vibrio,Yersinia,Helicobacter,Moraxella. | Bacteria, pathogen, genome, Illumina short read, genotype, core genome multilocus, sequence typing, cgMLST, cgMLST sequence, bacterial strain mapping, visualizing genomic variation, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: University of Warwick; Coventry; United Kingdom |
Biotechnology and Biological Sciences Research Council ; Wellcome Trust |
Restricted | biotools:Enterobase | https://bio.tools/EnteroBase | SCR_019019 | 2026-08-03 09:37:23 | 233 | |||||||
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Daring Nucleic Adventures - genegeek Resource Report Resource Website |
Daring Nucleic Adventures - genegeek (RRID:SCR_005215) | DNA, DNA - genegeek | narrative resource, data or information resource, blog | Hi. I''m genegeek (aka Catherine Anderson). I realized during my PostDoc that I preferred learning and explaining new results to doing science so I started a non-traditional career of teaching and outreach. I''ll be using this space to explore public perception of genetics and other cool molecular biology stuff. I hope to add to the great discussions re: new science discoveries and general understanding of genetics. I''ve been running an outreach program and enjoy talking to non-experts about their opinions and understanding. I hope my enthusiasm for the topics can come through the screen. My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution. | genetics, molecular biology, dna, science, genome, education |
is used by: NIF Data Federation is used by: Integrated Blogs has parent organization: LabSpaces |
nlx_144219 | SCR_005215 | Daring Nucleic Adventures | 2026-08-03 09:32:37 | 0 | ||||||||
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International Knockout Mouse Consortium Resource Report Resource Website 50+ mentions |
International Knockout Mouse Consortium (RRID:SCR_005574) | IKMC | data or information resource, database | Database of the international consortium working together to mutate all protein-coding genes in the mouse using a combination of gene trapping and gene targeting in C57BL/6 mouse embryonic stem (ES) cells. Detailed information on targeted genes is available. The IKMC includes the following programs: * Knockout Mouse Project (KOMP) (USA) ** CSD, a collaborative team at the Children''''s Hospital Oakland Research Institute (CHORI), the Wellcome Trust Sanger Institute and the University of California at Davis School of Veterinary Medicine , led by Pieter deJong, Ph.D., CHORI, along with K. C. Kent Lloyd, D.V.M., Ph.D., UC Davis; and Allan Bradley, Ph.D. FRS, and William Skarnes, Ph.D., at the Wellcome Trust Sanger Institute. ** Regeneron, a team at the VelociGene division of Regeneron Pharmaceuticals, Inc., led by David Valenzuela, Ph.D. and George D. Yancopoulos, M.D., Ph.D. * European Conditional Mouse Mutagenesis Program (EUCOMM) (Europe) * North American Conditional Mouse Mutagenesis Project (NorCOMM) (Canada) * Texas A&M Institute for Genomic Medicine (TIGM) (USA) Products (vectors, mice, ES cell lines) may be ordered from the above programs. | gene, knock out mouse, chromosome, allele, c57bl/6, embryonic stem cell, vector, mutant, es cell, genome, targeting, gene list, FASEB list |
is related to: Texas A and M Institute for Genomic Medicine is related to: European Mouse Mutant Archive is related to: CMMR - Canadian Mouse Mutant Repository is parent organization of: EUCOMMTOOLS is parent organization of: North American Conditional Mouse Mutagenesis Project is parent organization of: European Conditional Mouse Mutagenesis Program is parent organization of: Knockout Mouse Project |
European Union ; NHGRI HG004074 |
PMID:22968824 PMID:21677750 |
nlx_146200 | SCR_005574 | 2026-08-03 09:32:52 | 68 | |||||||
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SwissRegulon Resource Report Resource Website 10+ mentions |
SwissRegulon (RRID:SCR_005333) | SwissRegulon | data or information resource, database | A database of genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including: * Experimentally determined binding sites reported in the literature. * Known sequence-specificities of transcription factors. * ChIP-chip and ChIP-seq data. * Alignments of orthologous non-coding regions. Predictions were made using the PhyloGibbs, MotEvo, IRUS and ISMARA algorithms developed in their group, depending on the data available for each organism. Annotations can be viewed in a Gbrowse genome browser and can also be downloaded in flat file format. | genome, binding site, transcription factor, genome-wide annotation, annotation, chip-chip, chip-seq, non-coding region, promoter, motif, transcript, regulatory motif, genome browser, FASEB list |
is listed by: OMICtools has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:23180783 PMID:17130146 |
Acknowledgement requested | nif-0000-03524, OMICS_00543 | SCR_005333 | SwissRegulon Database | 2026-08-03 09:32:39 | 44 | ||||||
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TranspoGene Resource Report Resource Website 1+ mentions |
TranspoGene (RRID:SCR_005634) | data or information resource, database | A publicly available database of Transposed elements (TEs) which are located within protein-coding genes of 7 organisms: human, mouse, chicken, zebrafish, fruilt fly, nematode and sea squirt. Using TranspoGene the user can learn about the many aspects of the effect these TEs have on their hosting genes, such as: exonization events (including alternative splicing-related data), insertion of TEs into introns, exons, and promoters, specific location of the TE over the gene, evolutionary divergence of the TE from its consensus sequence and involvement in diseases. TranspoGene database is quickly searchable through its website, enables many kinds of searches and is available for download. TranspoGene contains information regarding specific type and family of the TEs, genomic and mRNA location, sequence, supporting transcript accession and alignment to the TE consensus sequence. The database also contains host gene specific data: gene name, genomic location, Swiss-Prot and RefSeq accessions, diseases associated with the gene and splicing pattern. The TranspoGene and microTranspoGene databases can be used by researchers interested in the effect of TE insertion on the eukaryotic transcriptome. | element, eukaryotic, evolutionary, exon, exonization, family, fruit fly, gene, genome, alternative, chicken, coding, disease, divergence, genomic, hosting, human, human genome databases, intron, location, map, maps, mouse, mrna, nematode, organism, pattern, promoter, protein, sea squirt, sequence, splicing, transcript, transcriptome, transposed, viewers, worm, zebrafish | has parent organization: Tel Aviv University; Ramat Aviv; Israel | nif-0000-03579 | SCR_005634 | TranspoGene | 2026-08-03 09:32:54 | 9 | |||||||||
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Systems Transcriptional Activity Reconstruction Resource Report Resource Website 5000+ mentions |
Systems Transcriptional Activity Reconstruction (RRID:SCR_005622) | STAR | service resource, data or information resource, database | A next-generation web-based application that aims to provide an integrated solution for both visualization and analysis of deep-sequencing data, along with simple access to public datasets. | genome browser, genome, next generation sequence, visualization, FASEB list |
is used by: CIRCexplorer is listed by: OMICtools is related to: star-for-criu has parent organization: University of California at San Diego; California; USA |
Account required, Or Guest login | OMICS_00895 | SCR_005622 | Systems Transcriptional Activity Reconstruction Genome Browser, Systems Transcriptional Activity Reconstruction, STAR Genome Browser | 2026-08-03 09:32:54 | 6475 |
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