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 | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Visualization and Analysis of Networks containing Experimental Data (VANTED) Resource Report Resource Website 10+ mentions |
Visualization and Analysis of Networks containing Experimental Data (VANTED) (RRID:SCR_001138) | VANTED | data visualization software, data analysis software, software application, software resource, data processing software | Software tool for extendable network visualization and analysis for the life sciences. It is Java-based and allows users to create, edit and map data onto existing or new networks. Experimental datasets can be visualized on network elements as graphical charts to show time series data or data of different treatments, as well as environmental conditions in the context of the underlying biological processes. Users can utilize built-in statistical algorithms to evaluate mapped data. | binary executable, simulation software, signal processing software, java, network visualization, statistical analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:23140568 | Open source | biotools:vanted, nif-0000-00373 | https://bitbucket.org/vanted-dev/vanted/src, https://bio.tools/vanted | http://vanted.ipk-gatersleben.de/ | SCR_001138 | Visualization and Analysis of Networks containing Experimental Data, VANTED v2 | 2026-07-31 09:25:01 | 14 | ||||
|
AceDB Resource Report Resource Website 10+ mentions |
AceDB (RRID:SCR_010671) | data or information resource, database, service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software genome database management system. | genome database management system, genome database, management system, |
is listed by: Debian is listed by: OMICtools is related to: ESTHER has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
DOI:10.1109/5992.764215 | THIS RESOURCE IS NO LONGER IN SERVICE. | nlx_75315, OMICS_15828 | https://sources.debian.org/src/acedb-other/ | SCR_010671 | A C. elegans DataBase | 2026-07-30 09:28:35 | 12 | ||||||
|
MethBase Resource Report Resource Website 1+ mentions |
MethBase (RRID:SCR_017487) | data or information resource, database, service resource | Central reference methylome database created from public BS-seq datasets. Provides methylation level at individual sites, regions of allele specific methylation, hypo- or hyper-methylated regions, partially methylated regions, and detailed meta data and summary statistics. | Methylome, database, public, BSseq, dataset, methylation, site, region, allele, specific, metadata, statistics, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
Free, Freely available | BioTools:MethBase, biotools:Methbase | https://bio.tools/MethBase, https://bio.tools/MethBase, https://bio.tools/MethBase | SCR_017487 | MethBase: a reference methylome database | 2026-07-30 09:30:10 | 1 | |||||||
|
PhenoFam Resource Report Resource Website |
PhenoFam (RRID:SCR_000640) | PhenoFam | software resource, software application | A web-based application that performs gene set enrichment analysis (GSEA) by employing structural and functional information on families of protein domains as annotation terms. | java, javascript, gene, gene set enrichment analysis, structure, function, protein domain, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20478033 | Free, Available for download, Freely available | OMICS_02230, biotools:phenofam | https://bio.tools/phenofam | SCR_000640 | 2026-07-30 09:25:59 | 0 | ||||||
|
FLOSS Resource Report Resource Website |
FLOSS (RRID:SCR_000836) | FLOSS | software resource, software application | Software application that performs ordered subset analysis using MERLIN's ouput .lod file created with the --perFamily option. Ordered subset analysis uses covariate information to identify a more homogenous subset of families for linkage analysis. The homogeneous subset of families does not need to be specified a priori, and the covariates can include environmental exposures, quantitative traits, or linkage scores at another locus in the genome. The evidence for linkage is evaluated with a permutation test. (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
biotools:floss, nlx_154319 | https://bio.tools/floss | SCR_000836 | FLexible Ordered SubSet analysis | 2026-07-30 09:26:03 | 0 | |||||||
|
ReadqPCR Resource Report Resource Website |
ReadqPCR (RRID:SCR_000030) | software resource, software application, standalone software | A software package that provides functions to read raw RT-qPCR data of different platforms. | standalone software, mac os x, unix/linux, windows, r, data import, gene expression, microtitre plate assay, qpcr, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: University College London; London; United Kingdom |
PMID:22748112 | Free, Available for download, Freely available | biotools:readqpcr, OMICS_03936 | https://bio.tools/readqpcr | SCR_000030 | ReadqPCR - Read qPCR data | 2026-07-30 09:25:53 | 0 | ||||||
|
metabnorm Resource Report Resource Website |
metabnorm (RRID:SCR_001266) | software resource, software application, standalone software | Software tool as mixed model normalization method for metabolomics data.Uses normalization approach based on mixed model, with simultaneous estimation of correlation matrix. | Metabolomics datasets, corelation, normalization, identifying metabolites, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
Cancer Research UK Cambridge Institute ; Erik and Edith Fernström foundation ; Cancer Research UK |
PMID:24711654 | Free, Available for download, Freely available | OMICS_03548, biotools:metabnorm | https://bio.tools/metabnorm | SCR_001266 | 2026-07-30 09:26:12 | 0 | ||||||
|
e-Driver Resource Report Resource Website 1+ mentions |
e-Driver (RRID:SCR_002674) | software resource, software application, standalone software | Software tool to identify cancer driver genes based on linear annotations of biological regions such as protein domains.Uses information on three-dimensional structures of mutated proteins to identify specific structural features. Then algorithm analyzes whether these features are enriched in cancer somatic mutations and are candidate driver genes. | Identify cancer driver genes, candidate driver genes, perl, protein, mutated proteins, cancer somatic mutations, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Cancer | PMID:25064568 | Free, Available for download, Freely available | biotools:e-Driver, OMICS_05288 | https://bio.tools/e-Driver | SCR_002674 | 2026-07-30 09:26:38 | 5 | ||||||
|
DINDEL Resource Report Resource Website 10+ mentions |
DINDEL (RRID:SCR_001827) | Dindel | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software program for calling small indels from short-read sequence data ("next generation sequence data"). It is currently designed to handle only Illumina data. Dindel takes BAM files with mapped Illumina read data and enables researchers to detect small indels and produce a VCF file of all the variant calls. It has been written in C++ and can be used on Linux-based and Mac computers (it has not been tested on Windows operating systems). | indel, short-read, next generation sequence, illumina, gene, genetic, genomic, c++, linux, macos, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
PMID:20980555 DOI:10.1101/gr.112326.110 |
THIS RESOURCE IS NO LONGER IN SERVICE | , nlx_154283, OMICS_00096, biotools:dindel | https://bio.tools/dindel, https://sources.debian.org/src/dindel/ | http://www.sanger.ac.uk/resources/software/dindel/ | SCR_001827 | Dindel: Accurate indel calls from short-read data | 2026-07-30 09:26:20 | 44 | ||||
|
IgBLAST Resource Report Resource Website 500+ mentions |
IgBLAST (RRID:SCR_002873) | software resource, software application | THIS RESOURCE IS NO LONGER IN SERVICE.Documented on January 4,2023. IgBLAST was developed at NCBI to facilitate analysis of immunoglobulin V region sequences in GenBank. In addition to performing a regular BLAST search, IgBLAST has several additional functions: - Reports the germline V, D and J gene matches to the query sequence. - Annotates the immunoglobulin domains (FWR1 through FWR3). - Matches the returned hits (for databases other than germline genes) to the closest germline V genes, making it easier to identify related sequences. - Reveals the V(D)J junction details such as nucleotide homology between the ends of V(D)J segments and N nucleotide insertions. D and J gene reporting is only for nucleotide sequence search and requires a stretch of five or more nucleotide identity between the query and D or J genes. Sponsors: This resource is supported by the National Center for Biotechnology Information, a division of the U.S. National Library of Medicine. | gene, analysis, domain, homology, immunoglobulin v, nucleotide, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools has parent organization: NCBI |
PMID:23671333 | Free, Freely available | nif-0000-25554, biotools:igblast, OMICS_06083 | https://bio.tools/igblast, https://sources.debian.org/src/ncbi-igblast/ | SCR_002873 | IgBLAST | 2026-07-30 09:26:43 | 609 | ||||||
|
PEDIGRAPH Resource Report Resource Website 10+ mentions |
PEDIGRAPH (RRID:SCR_001938) | Pedigraph | software resource, software application | A pedigree visualization program specifically designed to draw large, complex pedigrees. (entry from Genetic Analysis Software) Options include: * Full pedigree * Summarization * Extraction of individual pedigrees * Inbreeding calculation * Coancestry coefficient calculation * Color control * Drawing size * Page size and margins * Drawing styles | gene, genetic, genomic, c, c++, ms-windows, linux, pedigree, java, bio.tools |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: University of Minnesota Twin Cities; Minnesota; USA |
PMID:14986440 | Acknowledgement required, Copyrighted | biotools:pedigraph, OMICS_00212, nlx_154519 | https://bio.tools/pedigraph | SCR_001938 | 2026-07-30 09:26:23 | 17 | ||||||
|
Apollo Resource Report Resource Website 100+ mentions |
Apollo (RRID:SCR_001936) | Apollo | software resource, software application | A standalone Java application with a GUI (graphical user interface) for editing genome annotations. Like GBrowse, it allows users to scroll and zoom in on areas of interest in a sequence; authorized users can edit annotations and write the changes back to the underlying database. Apollo can run off GFF3 or a Chado database, and it can also integrate with remote services, such as BLAST and Primer BLAST analyses. | java, genome annotation, genome, annotation, windows, mac os x, linux, solaris, unix, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Generic Model Organism Database Project |
PMID:19439563 PMID:12537571 DOI:10.1186/gb-2002-3-12-research0082 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_11761, biotools:apollo, OMICS_01933 | https://bio.tools/apollo, https://sources.debian.org/src/aragorn/ | SCR_001936 | 2026-07-30 09:26:19 | 274 | ||||||
|
PsychoPy Resource Report Resource Website 1000+ mentions |
PsychoPy (RRID:SCR_006571) | PsychoPy | software resource, software application | Open source application to allow the presentation of stimuli and collection of data for a wide range of neuroscience, psychology and psychophysics experiments. It is intended as a free, powerful alternative to Presentation or e-Prime. | console (text based), experimental control, freebsd, linux, macos, microsoft, magnetic resonance, posix/unix-like, python, win32 (ms windows), windows, neuroscience, psychology, psychophysics |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian has parent organization: University of Nottingham; Nottingham; United Kingdom |
PMID:17254636 PMID:19198666 |
GNU General Public License | nlx_155928 | http://www.nitrc.org/projects/psychopy, https://sources.debian.org/src/psychopy/ | SCR_006571 | PsychoPy - Psychology software in Python | 2026-07-30 09:27:25 | 1975 | |||||
|
VarScan Resource Report Resource Website 1000+ mentions |
VarScan (RRID:SCR_006849) | VarScan, VarScan 2 | software resource, software application | Platform-independent, technology-independent software tool for identifying SNPs and indels in massively parallel sequencing of individual and pooled samples. Given data for a single sample, VarScan identifies and filters germline variants based on read counts, base quality, and allele frequency. Given data for a tumor-normal pair, VarScan also determines the somatic status of each variant (Germline, Somatic, or LOH) by comparing read counts between samples. (entry from Genetic Analysis Software). | gene, genetic, genomic, java, illumina, solid, life/pgm, roche/454, next-generation sequencing, variant, mutation caller, exome, whole-genome, snp, copy number alteration, somatic mutation, subclonal mutation, mutation, bio.tools |
is listed by: Genetic Analysis Software is listed by: Debian is listed by: bio.tools is organization facet of: Washington University in St. Louis; Missouri; USA |
PMID:22300766 PMID:19542151 DOI:10.1101/gr.129684.111 |
Free, Available for download, Freely available | , nlx_154687, biotools:varscan, OMICS_00094 | http://varscan.sourceforge.net/, http://dkoboldt.github.io/varscan/, https://bio.tools/varscan, https://sources.debian.org/src/varscan/ | http://genome.wustl.edu/software/varscan, http://tvap.genome.wustl.edu/tools/varscan/ | SCR_006849 | Varscan2, VarScan - variant detection in massively parallel sequencing data, Varscan | 2026-07-30 09:27:28 | 1769 | ||||
|
GoSurfer Resource Report Resource Website 1+ mentions |
GoSurfer (RRID:SCR_005789) | GoSurfer | software resource, software application | GoSurfer uses Gene Ontology (GO) information to analyze gene sets obtained from genome-wide computations or microarray analyses. GoSurfer is a graphical interactive data mining tool. It associates user input genes with GO terms and visualizes such GO terms as a hierarchical tree. Users can manipulate the tree output by various means, like setting heuristic thresholds or using statistical tests. Significantly important GO terms resulted from a statistical test can be highlighted. All related information are exportable either as texts or as graphics. Platform: Windows compatible | gene, gene ontology, genome-wide, microarray, graph, data mining, statistical analysis, bioinformatics, genomics, gene cluster, multiple hypothesis testing, false discovery rate, bio.tools |
is listed by: Gene Ontology Tools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: University of Illinois at Urbana-Champaign; Illinois; USA has parent organization: Harvard T.H. Chan School of Public Health |
PMID:15702958 | Free for academic use | biotools:gosurfer, nlx_149268 | http://www.gosurfer.org, https://bio.tools/gosurfer | http://bioinformatics.bioen.illinois.edu/gosurfer/index.htm | SCR_005789 | 2026-07-30 09:27:14 | 2 | |||||
|
LDSELECT Resource Report Resource Website 10+ mentions |
LDSELECT (RRID:SCR_007010) | LDSELECT | software resource, software application | Software program that analyzes patterns of linkage disequilibrium (LD) between polymorphic sites in a locus, and bins the SNPs on the basis of a threshold level of LD as measured by r2. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:ld_select, nlx_154426 | https://bio.tools/ld_select | SCR_007010 | 2026-07-30 09:27:34 | 15 | |||||||
|
BOMP: beta-barrel Outer Membrane protein Predictor Resource Report Resource Website 1+ mentions |
BOMP: beta-barrel Outer Membrane protein Predictor (RRID:SCR_007268) | software resource, software application | BOMP is a tool for prediction of beta-barrel integral outer membrane proteins. The user may submit a list of proteins, and receive a list of predicted BOMPs. The program, called the beta-barrel Outer Membrane protein Predictor (BOMP), is based on two separate components to recognize integral beta-barrel proteins. The first component is a C-terminal pattern typical of many integral beta-barrel proteins. The second component calculates an integral beta-barrel score of the sequence based on the extent to which the sequence contains stretches of amino acids typical of transmembrane -strands. To use the BOMP tool simply paste your fasta-formatted sequences into the text area, or choose a file which contains sequences. Then hit the submit button. It is possible to perform a BLAST search parallel with the predictions, which may be suitable in some cases. Using the BLAST search will however increase the running time substantially. Sponsors: This work was supported in part by grants from the Norwegian Research Council [SUP 140785/420 (GABI); FUGE/CBU151899/ISO], and the Meltzer Foundation, University of Bergen. Keywords: Beta-barrel, Membrane, Protein, Program, Software, Beta strand, Bacteria, | bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Bergen; Bergen; Norway |
biotools:bomp, nif-0000-30236 | https://bio.tools/bomp | SCR_007268 | BOMP Program | 2026-07-30 09:27:35 | 5 | ||||||||
|
PEDIGREEQUERY Resource Report Resource Website 1+ mentions |
PEDIGREEQUERY (RRID:SCR_009041) | PEDIGREEQUERY | software resource, software application | Software application that allows drawing pedigrees with a difficult structure, those containing consanguinity loops, and those individuals with multiple mates or several related families (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154007, biotools:pedcut | https://bio.tools/pedcut | SCR_009041 | 2026-07-30 09:28:05 | 1 | ||||||||
|
FASTSLINK Resource Report Resource Website 10+ mentions |
FASTSLINK (RRID:SCR_008664) | FASTSLINK | software resource, software application | Software application that is a faster version of SLINK (entry from Genetic Analysis Software) | gene, genetic, genomic, c, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: SLINK is related to: SUP |
nlx_154312, biotools:snpcaller | https://bio.tools/snpcaller | SCR_008664 | faster SLINK | 2026-07-30 09:28:00 | 12 | |||||||
|
PEDPEEL Resource Report Resource Website |
PEDPEEL (RRID:SCR_008436) | PEDPEEL | software resource, software application | Software program that prepares pedigree data for calculation of Elston-Stewarts'' likelihood function. It finds an optimal way to peel a pedigree and returns text file containing 7 description arrays (entry from Genetic Analysis Software) | gene, genetic, genomic, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154524, biotools:pedpeel | https://bio.tools/pedpeel | SCR_008436 | 2026-07-30 09:27:48 | 0 |
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
