Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
deepSNV Resource Report Resource Website 10+ mentions |
deepSNV (RRID:SCR_006214) | deepSNV | software resource | Software package that provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs (single nucleotide variants). | data import, genetic variability, genetics, snp, sequencing, single nucleotide variant, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24443148 | GNU General Public License, v3 | OMICS_02239, biotools:deepsnv | https://bio.tools/deepsnv | SCR_006214 | deepSNV - Detection of subclonal SNVs in deep sequencing experiments | 2026-09-05 06:25:49 | 34 | |||||
|
PHYLIP Resource Report Resource Website 1000+ mentions |
PHYLIP (RRID:SCR_006244) | PHYLIP | data processing software, software application, software resource, source code | A free package of software programs for inferring phylogenies (evolutionary trees). The source code is distributed (in C), and executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp/Vista), Mac OS X, and Linux systems. Older executables are also available for Mac OS 8 or 9 systems. | phylogeny prediction, evolutionary tree, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Washington; Seattle; USA works with: PAML |
NSF ; NIGMS ; DOE |
Free | nif-0000-06708, OMICS_04240, biotools:phylip | https://bio.tools/phylip, https://sources.debian.org/src/phylip/ | SCR_006244 | PHYLogeny Inference Package | 2026-09-05 06:25:49 | 3544 | |||||
|
ScerTF Resource Report Resource Website 10+ mentions |
ScerTF (RRID:SCR_006121) | ScerTF | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | Catalog of over 1,200 position weight matrices (PWMs) for 196 different yeast transcription factors (TFs). They've curated 11 literature sources, benchmarked the published position-specific scoring matrices against in-vivo TF occupancy data and TF deletion experiments, and combined the most accurate models to produce a single collection of the best performing weight matrices for Saccharomyces cerevisiae. ScerTF is useful for a wide range of problems, such as linking regulatory sites with transcription factors, identifying a transcription factor based on a user-input matrix, finding the genes bound/regulated by a particular TF, and finding regulatory interactions between transcription factors. Enter a TF name to find the recommended matrix for a particular TF, or enter a nucleotide sequence to identify all TFs that could bind a particular region. | binding site, transcription factor, regulatory site, gene, regulation, regulatory interaction, matrix, nucleotide sequence, dna sequence, yeast, position weight matrix, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA |
NIGMS R01 GM078222; NHGRI HG00249 |
PMID:22140105 | biotools:scertf, nlx_151599, OMICS_00542 | http://ural.wustl.edu/ScerTF, https://bio.tools/scertf | http://ural.wustl.edu/TFDB/ | SCR_006121 | 2026-09-05 06:25:47 | 19 | |||||
|
SitEx Resource Report Resource Website 1+ mentions |
SitEx (RRID:SCR_006122) | SitEx | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 19,2019. Analyzing protein structure projection on exon-intron structure of corresponding gene through years led to several fundamental conclusions about structural and functional organization of the protein. According to these results we decided to map the protein functional sites. So we created the database SitEx that keep the information about this mapping and included the BLAST search and 3D similar structure search using PDB3DScan for the polypeptide encoded by one exon, participating in organizing the functional site. This will help: # to study the positions of the functional sites in exon structure; # to make the complex analysis of the protein function; # to exposure the exons that took part in exon shuffling and came from bacterial genomes; # to study the peculiarities of coding the polypeptide structures. Currently, SitEx contains information about 9994 functional sites presented in 2021 proteins described in proteomes of 17 organisms. | projection, protein, functional site, exon, blast, structure, function, gene, amino acid, encoding gene, proteome, ligand, data set, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Institute of Cytology and Genetics of the Siberian Branch of the RAS; Novosibirsk; Russia |
Ministry of Science and Education 14.740.11.0001; Ministry of Science and Education 07.514.11.4003; Interdisciplinary Integrative Project 35 of SB RAS ; Russian Foundation for Basic Research 11-04-92712; EU-FP7 260429; Program of RAS ; DAAD Leonard Euler Program Grant |
PMID:22139920 | THIS RESOURCE IS NO LONGER IN SERVICE. | biotools:sitex, nlx_151602 | https://bio.tools/sitex | SCR_006122 | SitEx Database | 2026-09-05 06:25:47 | 1 | ||||
|
Predictive Networks Resource Report Resource Website |
Predictive Networks (RRID:SCR_006110) | PN | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource, source code | A flexible, open-source, web-based application and data services framework that enables the integration, navigation, visualization and analysis of gene interaction networks. The primary goal of PN is to allow biomedical researchers to evaluate experimentally derived gene lists in the context of large-scale gene interaction networks. The PN analytical pipeline involves two key steps. The first is the collection of a comprehensive set of known gene interactions derived from a variety of publicly available sources. The second is to use these ''known'' interactions together with gene expression data to infer robust gene networks. The regression-based network inference algorithm creates a graph of gene interactions in which cycles may be present (but no self-loops). Based on information-theoretic techniques, a causal gene interaction network is inferred from both prior knowledge (interactions extracted from biomedical literature and structured biological databases) and gene expression data. A prediction model is fitted for each gene, given its parents, enabling assessment of the predictive ability of the network model. | gene interaction network, gene, interaction, gene expression, graph, visualization, gene interaction, gene network, predictive network analysis, model, bio.tools |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute has parent organization: SourceForge |
NLM 1R01LM010129 | PMID:22096235 | Apache License, v2 | nlx_151582, biotools:predictivenetworks | https://bio.tools/predictivenetworks | SCR_006110 | 2026-09-05 06:25:47 | 0 | |||||
|
SpliceDisease Resource Report Resource Website 1+ mentions |
SpliceDisease (RRID:SCR_006130) | SpliceDisease | data or information resource, data repository, database, service resource, storage service resource | Curated database of experimentally supported data of RNA Splicing mutation and disease. The RNA Splicing mutations include cis-acting mutations that disrupt splicing and trans-acting mutations that affecting RNA-dependent functions that cause disease. Information such as EntrezGeneID, gene genomic sequence, mutation (nucleotide substitutions, deletions and insertions), mutation location within the gene, organism, detailed description of the splicing mutation and references are also given. Users are able to submit new entries to the database. This database integrating RNA splicing and disease associations would be helpful for understanding not only the RNA splicing but also its contribution to disease. In SpliceDisease database, they manually curated 2337 splicing mutation disease entries involving 303 genes and 370 diseases, which have been supported experimentally in 898 publications. The SpliceDisease database provides information including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference PubMed ID and detailed description for the relationship among gene mutations, splicing defects and diseases. They standardized the names of the diseases and genes and provided links for these genes to NCBI and UCSC genome browser for further annotation and genomic sequences. For the location of the mutation, they give direct links of the entry to the respective position/region in the genome browser. | rna splicing, mutation, disease, gene, genomic sequence, nucleotide substitution, deletion, insertion, mutation location, splicing mutation, nucleotide, disease association, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Peking University; Beijing; China |
National Natural Science Foundation of China 81001481 | PMID:22139928 | The community can contribute to this resource | biotools:splicedisease_db, nlx_151614 | https://bio.tools/splicedisease_db | SCR_006130 | Splice Disease, SpliceDisease Database Site, Splice Disease Database, SpliceDisease Database | 2026-09-05 06:25:47 | 2 | ||||
|
ChemSpider Resource Report Resource Website 1000+ mentions |
ChemSpider (RRID:SCR_006360) | ChemSpider | data access protocol, data or information resource, database, mobile app, service resource, software application, software resource, web service | Collection of chemical structures. Provides access to structures, properties and associated information from hundreds of data sources to find compounds of interest and provides services to improve this data by curation and annotation and to integrate it with users applications. | collection, chemical, structure, property, data, compound, bio.tools, FASEB list |
is used by: Open PHACTS is used by: GEROprotectors is listed by: re3data.org is listed by: bio.tools is listed by: Debian has parent organization: Royal Society of Chemistry |
GGA Software Services ; Waters |
Free, Freely available, Registration required for some sites | nlx_152101, biotools:chemspider, r3d100010205 | https://bio.tools/chemspider, https://doi.org/10.17616/R38P4P | SCR_006360 | 2026-09-05 06:25:52 | 2112 | ||||||
|
QCGWAS Resource Report Resource Website 1+ mentions |
QCGWAS (RRID:SCR_006408) | QCGWAS | software resource | Software tools for (automated and manual) quality control of the results of Genome Wide Association Studies. | quality control, genome wide association study, windows, os x, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24395754 | GNU General Public License, v3 or later | OMICS_02203, biotools:qcgwas | https://bio.tools/qcgwas | SCR_006408 | QCGWAS: Quality Control of Genome Wide Association Study results, Quality Control of Genome Wide Association Study | 2026-09-05 06:25:53 | 7 | |||||
|
Jalview Resource Report Resource Website 1000+ mentions |
Jalview (RRID:SCR_006459) | Jalview | software resource | A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure. | edit, analysis, annotation, multiple sequence alignment, wysiwyg, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Dundee; Scotland; United Kingdom |
BBSRC BBSB16542 | PMID:19151095 DOI:10.1093/bioinformatics/btp033 |
GNU General Public License, v3, Acknowledgement requested | OMICS_00885, biotools:Jalview | https://bio.tools/Jalview, https://sources.debian.org/src/jalview/ | SCR_006459 | 2026-09-05 06:25:54 | 4136 | |||||
|
SRAdb Resource Report Resource Website 10+ mentions |
SRAdb (RRID:SCR_006524) | SRAdb | software resource | Software package to make access to the compilation of metadata from NCBI SRA and tools associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: NCBI Sequence Read Archive (SRA) has parent organization: Bioconductor |
PMID:23323543 | Artistic License, v2 | biotools:sradb, OMICS_01032 | https://bio.tools/sradb | SCR_006524 | SRAdb - A compilation of metadata from NCBI SRA and tools | 2026-09-05 06:25:55 | 18 | |||||
|
NCBI Resource Report Resource Website 10000+ mentions |
NCBI (RRID:SCR_006472) | NCBI | nonprofit organization | A portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease. | biomedical, genomic, molecular biology, health, disease, database, computational biology, bio.tools |
is used by: NIF Data Federation is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: AmiGO is related to: NCBI Viral Genomes is related to: Clone DB is related to: PubReader is related to: OMIA - Online Mendelian Inheritance in Animals is related to: European Nucleotide Archive (ENA) is related to: Plant Co-expression Annotation Resource is related to: METAGENOTE is related to: Phyutility is related to: CaspBase is related to: Prokaryotic Genomes Automatic Annotation Pipeline has parent organization: National Library of Medicine is parent organization of: MedGen is parent organization of: dbSTS is parent organization of: PubMed Health is parent organization of: BLASTP is parent organization of: GQuery is parent organization of: BLASTN is parent organization of: GTEx eQTL Browser is parent organization of: BLASTX is parent organization of: Homology Maps Page is parent organization of: PEDHUNTER is parent organization of: Conserved Domain Database is parent organization of: NCBI Genome Survey Sequences Database is parent organization of: High Throughput Genomic Sequences Division is parent organization of: AceView is parent organization of: dbMHC is parent organization of: dbSNP is parent organization of: Entrez Gene is parent organization of: NCBI Genome is parent organization of: NCBI database of Genotypes and Phenotypes (dbGap) is parent organization of: GenBank is parent organization of: International HapMap Project is parent organization of: IgBLAST is parent organization of: Lowes Syndrome Mutation Database is parent organization of: HomoloGene is parent organization of: Influenza Virus Resource is parent organization of: Distant Regulatory Elements is parent organization of: e-PCR is parent organization of: MapViewer is parent organization of: Primer-BLAST is parent organization of: dbVar is parent organization of: NCBI Taxonomy is parent organization of: NCBI Protein Database is parent organization of: Gene Reference into Function is parent organization of: Protein Clusters is parent organization of: RefSeq is parent organization of: TPA is parent organization of: GENSAT at NCBI - Gene Expression Nervous System Atlas is parent organization of: COBALT: Constraint-based Multiple Alignment Tool is parent organization of: PubMed Central is parent organization of: UniLib is parent organization of: NCBI Structure is parent organization of: PubChem is parent organization of: Anopheles gambiae (African malaria mosquito) genome view is parent organization of: UniGene is parent organization of: NLM Catalog is parent organization of: Entrez GEO Profiles is parent organization of: Nucleotide database is parent organization of: NCBI BioSystems Database is parent organization of: CBLAST is parent organization of: NCBI BioProject is parent organization of: NCBI Probe is parent organization of: PubMed is parent organization of: NCBI BioSample is parent organization of: NCBI Nucleotide is parent organization of: NCBI Structure: Cn3D is parent organization of: NCBI BLAST is parent organization of: IBIS: Inferred Biomolecular Interactions Server is parent organization of: NCBI Sequence Read Archive (SRA) is parent organization of: Gene Expression Omnibus (GEO) is parent organization of: NCBI Popset is parent organization of: PIE the search is parent organization of: Genetic Testing Registry is parent organization of: NCBI Resource List is parent organization of: NCBI dbRBC is parent organization of: NCBI YouTube Channel is parent organization of: NCBI Epigenomics is parent organization of: ClinVar is parent organization of: Genome Reference Consortium is parent organization of: GeneReviews is parent organization of: Molecular Imaging and Contrast Agent Database is parent organization of: Consensus CDS is parent organization of: UniSTS is parent organization of: HIV-1 Human Protein Interaction Database is parent organization of: Assay Guidance Manual is parent organization of: Bookshelf is parent organization of: COG is parent organization of: Gene Expression Omnibus is parent organization of: Molecular Modelling DataBase is parent organization of: Organelle Genome Resources is parent organization of: SKY/M-FISH/CGH is parent organization of: dbEST is parent organization of: JournalReview.org is parent organization of: NCBI GenBank via FTP is parent organization of: PubChem Compound is parent organization of: Molecular Modeling DataBase is parent organization of: Vector Alignment Search Tool is parent organization of: PubChem BioAssay is parent organization of: NCBI Genome Workbench is parent organization of: TBLASTN is parent organization of: TBLASTX is parent organization of: Mega BLAST is parent organization of: Genetic Codes is parent organization of: HIV-1, Human Protein Interaction Database is parent organization of: PubReader is parent organization of: PubChem Substance is parent organization of: OMIA - Online Mendelian Inheritance in Animals is parent organization of: OMIM is parent organization of: 1000 Genomes: A Deep Catalog of Human Genetic Variation is parent organization of: GeneTests is parent organization of: NCBI Genome Survey Sequences Database is parent organization of: MagicBlast is parent organization of: RefSeq is parent organization of: Sequin is parent organization of: Batch Entrez is parent organization of: Entrez is parent organization of: tbl2asn is parent organization of: Whole Genome Shotgun (WGS) Project is parent organization of: Digital Differential Display (DDD) is parent organization of: BLASTClust is parent organization of: PASC is parent organization of: Open Reading Frame Finder is parent organization of: Genotyping works with: Human Mouse Disease Connection works with: A plasmid Editor works with: Database of genes related to Repeat Expansion Diseases |
Public, The community can contribute to this resource | nif-0000-00139, biotools:ncbi_resources | https://bio.tools/ncbi_resources | http://www.ncbi.nih.gov/ | SCR_006472 | National Center for Biotechnology Information, NCBI - National Center for Biotechnology Information | 2026-09-05 06:25:54 | 29053 | |||||
|
Phytozome Resource Report Resource Website 1000+ mentions |
Phytozome (RRID:SCR_006507) | Phytozome | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A comparative platform for green plant genomics. Families of orthologous and paralogous genes that represent the modern descendents of ancestral gene sets are constructed at key phylogenetic nodes. These families allow easy access to clade specific orthology / paralogy relationships as well as clade specific genes and gene expansions. As of release v9.1, Phytozome provides access to forty-one sequenced and annotated green plant genomes which have been clustered into gene families at 20 evolutionarily significant nodes. Where possible, each gene has been annotated with PFAM, KOG, KEGG, and PANTHER assignments, and publicly available annotations from RefSeq, UniProt, TAIR, JGI are hyper-linked and searchable., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | genome, genomics, plant, green plant, cluster sequence, alignment, gene, node, cluster, blast, blat, biomart, peptide homolog, gene ancestry, sequence, annotation, gene structure, gene family, genome organization, comparative genomics, physiology, comparative, bio.tools, FASEB list |
is listed by: re3data.org is listed by: Debian is listed by: bio.tools is related to: Plant Co-expression Annotation Resource has parent organization: DOE Joint Genome Institute has parent organization: Lawrence Berkeley National Laboratory |
Gordon and Betty Moore Foundation ; DOE DE-AC02-05CH11231 |
PMID:22110026 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:phytozome, nlx_151490, r3d100010850 | https://bio.tools/phytozome, https://doi.org/10.17616/R38021 | SCR_006507 | 2026-09-05 06:25:55 | 3189 | |||||
|
Gene Expression Database Resource Report Resource Website 50+ mentions |
Gene Expression Database (RRID:SCR_006539) | GXD | data or information resource, data repository, database, service resource, storage service resource | Community database that collects and integrates the gene expression information in MGI with a primary emphasis on endogenous gene expression during mouse development. The data in GXD are obtained from the literature, from individual laboratories, and from large-scale data providers. All data are annotated and reviewed by GXD curators. GXD stores and integrates different types of expression data (RNA in situ hybridization; Immunohistochemistry; in situ reporter (knock in); RT-PCR; Northern and Western blots; and RNase and Nuclease s1 protection assays) and makes these data freely available in formats appropriate for comprehensive analysis. There is particular emphasis on endogenous gene expression during mouse development. GXD also maintains an index of the literature examining gene expression in the embryonic mouse. It is comprehensive and up-to-date, containing all pertinent journal articles from 1993 to the present and articles from major developmental journals from 1990 to the present. GXD stores primary data from different types of expression assays and by integrating these data, as data accumulate, GXD provides increasingly complete information about the expression profiles of transcripts and proteins in different mouse strains and mutants. GXD describes expression patterns using an extensive, hierarchically-structured dictionary of anatomical terms. In this way, expression results from assays with differing spatial resolution are recorded in a standardized and integrated manner and expression patterns can be queried at different levels of detail. The records are complemented with digitized images of the original expression data. The Anatomical Dictionary for Mouse Development has been developed by our Edinburgh colleagues, as part of the joint Mouse Gene Expression Information Resource project. GXD places the gene expression data in the larger biological context by establishing and maintaining interconnections with many other resources. Integration with MGD enables a combined analysis of genotype, sequence, expression, and phenotype data. Links to PubMed, Online Mendelian Inheritance in Man (OMIM), sequence databases, and databases from other species further enhance the utility of GXD. GXD accepts both published and unpublished data. | endogenous, expression assay, expression data, expression image, gene expression, genes, image, immunohistochemistry, in situ reporter, knock in, mouse, mouse mutant, northern blot, nuclease protection assay, rna in situ hybridization, rnase protection assay, rt-pcr, western blot, endogenous gene expression, mouse development, gene, transcript, protein, annotation, development, embryonic mouse, bio.tools, FASEB list |
is listed by: GUDMAP Ontology is listed by: NIDDK Information Network (dkNET) is listed by: Debian is listed by: bio.tools is related to: VisiGene Image Browser is related to: Mouse Genome Informatics (MGI) is related to: Mouse Genome Informatics: The Mouse Gene Expression Information Resource Project is related to: EMAGE Gene Expression Database is related to: aGEM has parent organization: Jackson Laboratory is parent organization of: Adult Mouse Anatomy Ontology is parent organization of: Mouse Anatomical Dictionary Browser |
NICHD HD033745 | PMID:21062809 | Free | nif-0000-01253, biotools:gxd, SCR_017529 | https://bio.tools/gxd | SCR_006539 | Jackson Lab Gene Expression Database | 2026-09-05 06:25:56 | 58 | ||||
|
Rainbow Resource Report Resource Website 10+ mentions |
Rainbow (RRID:SCR_002724) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software developed to provide an ultra-fast and memory-efficient solution to clustering and assembling short reads produced by RAD-seq. | software, tool, clustering, assembling, short, read, restriction, site, DNA, sequence, analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22942077 DOI:10.1093/bioinformatics/bts482 |
Free, Freely available, Available for download | SCR_015992, OMICS_03722, biotools:rainbow | https://bio.tools/rainbow, https://sources.debian.org/src/bio-rainbow/ | SCR_002724 | RAD-seq: Restriction-site Associated DNA sequencing, Bio-rainbow, RAD-seq | 2026-09-05 06:24:52 | 41 | ||||||
|
Coding Potential Calculator Resource Report Resource Website 100+ mentions |
Coding Potential Calculator (RRID:SCR_002764) | CPC | analysis service resource, data analysis service, production service resource, service resource, software resource | A Support Vector Machine-based classifier to assesses the protein-coding potential of a transcript based on six biologically meaningful sequence features. CPC can discriminate coding from noncoding transcripts with high accuracy and speed. In addition to predicting the coding potential of the input transcripts, the CPC web server also graphically displays detailed sequence features and additional annotations of the transcript that may facilitate users' further investigation. The coding potential calculator tool reads FASTA data format as input. | fasta, transcript, protein coding, coding potential, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Peking University; Beijing; China |
PMID:17631615 | Free, Freely available | biotools:cpc, rid_000106 | https://bio.tools/cpc | SCR_002764 | 2026-09-05 06:24:53 | 225 | ||||||
|
rBiopaxParser Resource Report Resource Website 1+ mentions |
rBiopaxParser (RRID:SCR_002744) | software resource | A software package that provides a comprehensive set of functions for parsing, viewing and modifying BioPAX pathway data within R. At the moment BioPAX level 2 and level 3 are supported. | software package, mac os x, unix/linux, windows, data representation, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23274212 | Free, Freely available, Available for download | biotools:rbiopaxparser, OMICS_05211 | https://github.com/frankkramer/rBiopaxParser, https://bio.tools/rbiopaxparser | SCR_002744 | rBiopaxParser - Parses BioPax files and represents them in R | 2026-09-05 06:24:53 | 4 | ||||||
|
hot scan Resource Report Resource Website 1+ mentions |
hot scan (RRID:SCR_002840) | software resource | A free software to detect genomic regions unusually rich in translocation breakpoints. More generally, it may be used to detect a region that is unusually rich in a given character of a binary sequence. | software package, perl, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24860160 | Free, Freely available, Available for download | biotools:hot_scan, OMICS_05200 | https://bio.tools/hot_scan | SCR_002840 | hot_scan | 2026-09-05 06:24:54 | 6 | ||||||
|
GreenPhylDB Resource Report Resource Website 10+ mentions |
GreenPhylDB (RRID:SCR_002834) | GreenPhylDB | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource | A database designed for plant comparative and functional genomics based on complete genomes. It comprises complete proteome sequences from the major phylum of plant evolution. The clustering of these proteomes was performed to define a consistent and extensive set of homeomorphic plant families. Based on this, lists of gene families such as plant or species specific families and several tools are provided to facilitate comparative genomics within plant genomes. The analyses follow two main steps: gene family clustering and phylogenomic analysis of the generated families. Once a group of sequences (cluster) is validated, phylogenetic analyses are performed to predict homolog relationships such as orthologs and ultraparalogs. | comparative genomics, genome, functional genomics, genomics, gene family, homolog, bio.tools |
uses: Gene Ontology is listed by: bio.tools is listed by: Debian has parent organization: CIRAD |
PMID:20864446 | Free, Freely available, Available for download | biotools:greenphyldb, nif-0000-02928 | http://greenphyl.cirad.fr, http://www.greenphyl.org/v3/, https://bio.tools/greenphyldb | SCR_002834 | 2026-09-05 06:24:54 | 20 | ||||||
|
Cancer Genome Anatomy Project Resource Report Resource Website 100+ mentions |
Cancer Genome Anatomy Project (RRID:SCR_003072) | CGAP | data or information resource, portal, topical portal | Project to determine the gene expression profiles of normal, precancer, and cancer cells, whose generated resources are available to the cancer community. Interconnected modules provide access to all CGAP data, bioinformatic analysis tools, and biological resources allowing the user to find in silico answers to biological questions in a fraction of the time it once took in the laboratory. * Genes * Tissues * Pathways * RNAi * Chromosomes * SAGE Genie * Tools | gene, gene expression, normal cell, precancer cell, cancer cell, cell, genome, anatomy, gene expression profile, tissue, pathway, rnai, chromosome, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: National Cancer Institute is parent organization of: CGAP GO Browser |
Cancer, Normal, Precancer | NCI | Free, download Freely available | biotools:cgap, nif-0000-30468 | https://mitelmandatabase.isb-cgc.org/mb_search | SCR_003072 | Cancer Genome Anatomy Project (CGAP) | 2026-09-05 06:24:57 | 108 | ||||
|
Primer3Plus Resource Report Resource Website 1000+ mentions |
Primer3Plus (RRID:SCR_003081) | Primer3Plus | analysis service resource, data analysis service, production service resource, service resource, software resource, source code | A web interface to the Primer3 primer design program as an enhanced alternative for the CGI- scripts that come with Primer3. | primer, dna sequence, primer design, perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Primer3 has parent organization: Wageningen University and Research Centre; Gelderland; Netherlands |
Howard Hughes Medical Institute ; NHGRI R01-HG00257; NHGRI P50-HG00098 |
PMID:17485472 | Free, Freely available | biotools:primer3plus, OMICS_02347 | https://bio.tools/primer3plus | SCR_003081 | Primer3Plus - pick primers from a DNA sequence | 2026-09-05 06:24:57 | 1860 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the dkNET Resources search. From here you can search through a compilation of resources used by dkNET and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that dkNET has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on dkNET then you can log in from here to get additional features in dkNET such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into dkNET you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
Email: info_at_ dknet.org
