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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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leeHom Resource Report Resource Website 50+ mentions |
leeHom (RRID:SCR_002710) | software resource | Software program for the Bayesian reconstruction of ancient DNA fragments. The algorithm removes the adaptors and reconstructs the original DNA sequences using a Bayesian maximum a posteriori probability approach. | standalone software, illumina, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:25100869 | Free, Available for download, Freely available | biotools:leehom, OMICS_05254 | https://bio.tools/leehom | SCR_002710 | 2026-02-14 02:00:26 | 53 | |||||||
|
ANDES Resource Report Resource Website 10+ mentions |
ANDES (RRID:SCR_002791) | data processing software, data analysis software, software toolkit, software application, software resource | Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses. | deep sequencing, biomarker detection, statistical analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20633290 | Free, Freely available, Available for download | biotools:andes, OMICS_01119 | https://bio.tools/andes | SCR_002791 | Statistical tools for the Analyses of Deep Sequencing (ANDES), Statistical tools for the Analyses of Deep Sequencing, Statistical tools for the ANalyses of Deep Sequencing | 2026-02-14 02:00:32 | 25 | ||||||
|
NCBI database of Genotypes and Phenotypes (dbGap) Resource Report Resource Website 500+ mentions |
NCBI database of Genotypes and Phenotypes (dbGap) (RRID:SCR_002709) | dbGaP | data repository, storage service resource, data or information resource, service resource, database | Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits. | clinical, trial, genotype, interaction, homology, cell, morphology, interaction, phenotype, molecular diagnosis, genetic recombination, gold standard, bio.tools |
is used by: International Genomics of Alzheimers Project is used by: NIDDK Inflammatory Bowel Disease Genetics Consortium is used by: NIH Heal Project is used by: Genomic Data Commons Data Portal (GDC Data Portal) is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: OMICtools is listed by: re3data.org is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: NIDDK Central Repository is related to: eMERGE Network: electronic Medical Records and Genomics is related to: Framingham Heart Study is related to: PhenoExplorer is related to: Chronic Renal Insufficiency Cohort Study is related to: DbGaP Cleaner is related to: Psychiatric Genomics Consortium is related to: ISCA Consortium is related to: Allen Institute for Brain Science has parent organization: NCBI is parent organization of: Resource for Genetic Epidemiology Research on Adult Health and Aging |
NLM | PMID:24297256 PMID:17898773 |
Restricted | nif-0000-23342, OMICS_00263, biotools:dbgap, r3d100010788 | http://www.ncbi.nlm.nih.gov/sites/entrez?db=gap https://bio.tools/dbgap https://doi.org/10.17616/R3GS4K |
SCR_002709 | database of Genotypes and Phenotypes (dbGaP), dbGaP, NCBI, Database of Genotypes and Phenotypes | 2026-02-14 02:00:30 | 683 | ||||
|
Pathview Resource Report Resource Website 500+ mentions |
Pathview (RRID:SCR_002732) | software resource | A tool set for pathway-based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. | software package, r, differential expression, gene expression, gene set enrichment, genetics, graph, network, metabolomics, microarray, pathway, proteomics, rna-seq, sequencing, systems biology, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23740750 | Free, Freely available, Available for download | biotools:pathview, OMICS_05212 | http://pathview.r-forge.r-project.org/ https://bio.tools/pathview |
SCR_002732 | path view | 2026-02-14 02:00:30 | 520 | ||||||
|
SuperPred: Drug classification and target prediction Resource Report Resource Website |
SuperPred: Drug classification and target prediction (RRID:SCR_002691) | SuperPred | web service, data or information resource, data access protocol, software resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 24,2025. Publicly available web-server to predict medical indication areas based on properties and similarity of chemical compounds. The web-server translates a user-defined molecule into a structural fingerprint that is compared to about 6300 drugs, which are enriched by 7300 links to molecular targets of the drugs, derived through text mining followed by manual curation. Links to the affected pathways are provided. The similarity to the medical compounds is expressed by the Tanimoto coefficient that gives the structural similarity of two compounds. A similarity score higher than 0.85 results in correct ATC prediction for 81% of all cases. As the biological effect is well predictable, if the structural similarity is sufficient, the web-server allows prognoses about the medical indication area of novel compounds and to find new leads for known targets. The combination of physicochemical property and similarity searching provides the possibility to detect new biologically active compounds and novel targets for drug-like compounds. SuperPred can be applied for drug repositioning purposes, too. A further intention of SuperPred is to find side effects elicited by drugs caused through off-target hits. | drug, drug class, drug target, addiction, anatomical therapeutic chemical, application area, biological activity, chemical, chemical classification, chemical property, classification, compound, molecular target, molecule, nervous system, pathway, pharmacological property, physicochemical property, prediction, activity spectra, substance, structural similarity, structure, tanimoto coefficient, tanimoto score, target prediction, target-prediction server, therapeutic approach, therapeutic property, drug classification, target prediction, similarity score, target, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Charite - Universitatsmedizin Berlin; Berlin; Germany |
SFB 449 ; IRTG Berlin-Boston-Kyoto and Deutsche Krebshilfe. ; DFG |
PMID:18499712 PMID:24878925 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:superpred, nif-0000-00415 | https://bio.tools/superpred | SCR_002691 | 2026-02-14 02:00:29 | 0 | |||||
|
Rainbow Resource Report Resource Website 10+ mentions |
Rainbow (RRID:SCR_002724) | sequence analysis software, data processing software, data 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 | 2026-02-14 02:00:30 | 41 | ||||||
|
Coding Potential Calculator Resource Report Resource Website 100+ mentions |
Coding Potential Calculator (RRID:SCR_002764) | CPC | data analysis service, analysis service resource, 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 | 2026-02-14 02:00:31 | 198 | ||||||
|
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 | 2026-02-14 02:00:19 | 4 | ||||||
|
Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets Resource Report Resource Website 1000+ mentions |
Percolator: Semi-supervised learning for peptide identification from shotgun proteomics datasets (RRID:SCR_005040) | data or information resource, software resource, database | Percolator post-processes the results of a shotgun proteomics database search program, re-ranking peptide-spectrum matches so that the top of the list is enriched for correct matches. Shotgun proteomics uses liquid chromatography-tandem mass spectrometry to identify proteins in complex biological samples. We describe an algorithm, called Percolator, for improving the rate of peptide identifications from a collection of tandem mass spectra. Percolator uses semi-supervised machine learning to discriminate between correct and decoy spectrum identifications, correctly assigning peptides to 17% more spectra from a tryptic dataset and up to 77% more spectra from non-tryptic digests, relative to a fully supervised approach. The yeast-01 data is available in tab delimetered format. The SEQUEST parameter file and target database for the yeast and worm data are also available. | worm, yeast, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA |
PMID:17952086 | biotools:percolator, nlx_98814 | https://bio.tools/percolator | SCR_005040 | Percolator | 2026-02-14 02:00:48 | 2482 | |||||||
|
MBCluster.Seq Resource Report Resource Website 1+ mentions |
MBCluster.Seq (RRID:SCR_005079) | MBCluster.Seq | software resource | Software to cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24191069 | GNU General Public License, >/=v3 | OMICS_01417, biotools:mbcluster.seq | https://bio.tools/mbcluster.seq | SCR_005079 | MBCluster.Seq: Model-Based Clustering for RNA-seq Data | 2026-02-14 02:00:50 | 1 | |||||
|
GRASS Resource Report Resource Website 50+ mentions |
GRASS (RRID:SCR_005071) | GRASS | software resource | A generic algorithm for scaffolding next-generation sequencing assemblies. | next-generation sequencing, scaffolding, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22492642 | GNU General Public License, v3 | biotools:GRASS, OMICS_00043 | https://bio.tools/GRASS | SCR_005071 | GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies, GeneRic ASembly Scaffolder | 2026-02-14 02:00:48 | 89 | |||||
|
SINA Resource Report Resource Website 100+ mentions |
SINA (RRID:SCR_005067) | SINA | data analysis service, analysis service resource, production service resource, service resource, software resource | Service to align and optionally taxonomically classify your rRNA gene sequences. The results can be combined with any other sequences aligned by SINA or taken from the SILVA databases by concatenation of FASTA files or using the ARB MERGE tool. Note: Submission is currently limited to at most 1000 sequences of at most 6000 bases each. If your requirements exceed this limitation, get Opens internal link in current windowSINA for local installation. | alignment, taxonomic classification, rrna, gene sequence, fasta, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: SILVA is related to: ARB project has parent organization: Max Planck Institute for Marine Microbiology; Bremen; Germany |
PMID:22556368 | Free, Available for download, Freely available | OMICS_01438, biotools:sina | https://bio.tools/sina https://sources.debian.org/src/sina/ https://github.com/epruesse/SINA |
SCR_005067 | SINA Alignment Service, SILVA Incremental Aligner | 2026-02-14 02:01:02 | 369 | |||||
|
G-BLASTN Resource Report Resource Website |
G-BLASTN (RRID:SCR_005062) | G-BLASTN | software resource | A GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST. It can produce exactly the same results as NCBI-BLAST, and it also has very similar user commands. It also supports a pipeline mode, which can fully utilize the GPU and CPU resources when handling a batch of medium to large sized queries. | parallel computation 4, blast, alignment, nucleotide, gpu, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: NCBI BLAST has parent organization: Hong Kong Baptist University; Hong Kong; China has parent organization: SourceForge |
Hong Kong Baptist University; Hong Kong; China FRG2/11-12/158; NVIDIA |
PMID:24463183 | Free | OMICS_02263, biotools:g-blastn | http://sourceforge.net/projects/gblastn/ https://bio.tools/g-blastn |
SCR_005062 | 2026-02-14 02:01:02 | 0 | |||||
|
VFS Resource Report Resource Website 1+ mentions |
VFS (RRID:SCR_005138) | VFS | software resource | A versatile high-throughput sequencing (HTS) tool for discovering viral integration events and reconstruct fusion transcripts at single-base resolution. It combines soft-clipping information, read-pair analysis, and targeted de novo assembly to discover and annotate viral-human fusion events. A simple yet effective empirical statistical model is used to evaluate the quality of fusion breakpoints. Minimal user defined parameters are required. | ubuntu, debian, high-throughput sequencing, virus, reconstruct, fusion transcript, transcript, integration, fusion, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Chinese University of Hong Kong; Hong Kong; China |
PMID:23314323 | GNU General Public License, v3 | OMICS_00224, biotools:viralfusionseq | https://bio.tools/viralfusionseq | SCR_005138 | ViralFusionSeq, ViralFusionSeq (VFS) | 2026-02-14 02:01:03 | 1 | |||||
|
MMAPPR Resource Report Resource Website 1+ mentions |
MMAPPR (RRID:SCR_005092) | MMAPPR | software resource | A software analysis pipeline for mapping mutations using RNA-seq that works without parental strain information, without the requirement of a pre-existing snp map of the organism, and without erroneous assumptions that recombination occurs at the same frequency across the genome. In addition, it compensates for the considerable amount of noise in RNA-seq datasets and simultaneously identifies the region where the mutation lies and generates a list of putative coding region mutations in the linked genomic segment. MMAPPR can utilize RNA-seq datasets from isolated tissues or whole organisms that are often generated for phenotypic analysis and gene network analysis in novel mutants. | mutation, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
PMID:23299975 | Acknowledgement requested | OMICS_01361, biotools:mmappr | https://bio.tools/mmappr | SCR_005092 | Mutation Mapping Analysis Pipeline for Pooled RNA-seq | 2026-02-14 02:01:02 | 7 | |||||
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FusionMap Resource Report Resource Website 50+ mentions |
FusionMap (RRID:SCR_005242) | FusionMap | software resource | An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies. FusionMap runs under both Windows and Linux (requiring MONO) environments. Although it can run on 32 bit machine, it is recommended to run on 64-bit machine with 8GB RAM or more. If you have an ArrayStudio License, you can run the fusion detection easily through its GUI. | windows, linux, c#, fusion gene, next-generation sequencing, gene, reference indexing, read filtering, fusion alignment, reporting, alignment, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:21593131 | Free, Non-commercial | biotools:fusionmap, OMICS_00316 | https://bio.tools/fusionmap | SCR_005242 | 2026-02-14 02:01:05 | 88 | ||||||
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rQuant Resource Report Resource Website 1+ mentions |
rQuant (RRID:SCR_005150) | rQuant | software resource | Software for quantitative detection of alternative transcripts with RNA-Seq data. The method, based on quadratic programming, estimates biases introduced by experimental settings and is thus a powerful tool to reveal and quantify novel (alternative) transcripts. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy |
PMID:20551130 | biotools:rquant.web, OMICS_01286 | https://bio.tools/rquant.web | SCR_005150 | rQuant: quantitative detection of alternative transcripts with RNA-Seq data | 2026-02-14 02:01:03 | 1 | ||||||
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ShoRAH Resource Report Resource Website 10+ mentions |
ShoRAH (RRID:SCR_005211) | ShoRAH | software resource | A software package that allows for inference about the structure of a population from a set of short sequence reads as obtained from ultra-deep sequencing of a mixed sample. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. | linux, mac os x, windows, next-generation sequencing, c++, python, perl, structure, population, short sequence read, haplotype, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: ETH Zurich; Zurich; Switzerland |
PMID:21521499 | GNU General Public License, v3 | biotools:shorah, OMICS_00231 | https://bio.tools/shorah | SCR_005211 | Short Reads Assembly into Haplotypes, ShoRAH - Short Reads Assembly into Haplotypes | 2026-02-14 02:00:50 | 35 | |||||
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V-Phaser 2 Resource Report Resource Website 1+ mentions |
V-Phaser 2 (RRID:SCR_005212) | V-Phaser 2 | software resource | A software tool to call variants in genetically heterogeneous populations from ultra-deep sequence data. It combines information regarding the covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity. V-Phaser can reliably detect rare variants in diverse populations that occur at frequencies of <1%. V-Phaser 2 is a complete rewrite of the original V-Phaser. It contains a new model for length polymorphisms (indels) and incorporates paired end read information in its phasing model. The data access and probability computation sections of the code have also been highly optimized, resulting in substantial improvements in running time and memory usage. | variant, polymorphism, indel, virus, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
NIAID | PMID:24088188 | Free for academic use, Non-commercial, Http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/viral-genomics-software-license-v-phaser-2 | biotools:v-phaser, OMICS_00232 | https://bio.tools/v-phaser | SCR_005212 | 2026-02-14 02:01:03 | 2 | |||||
|
RNA-eXpress Resource Report Resource Website 1+ mentions |
RNA-eXpress (RRID:SCR_005167) | RNA-eXpress | software resource | Software designed as a user friendly solution to extract and annotate biologically important transcripts from next generation RNA sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Monash University; Melbourne; Australia |
PMID:23396121 | Acknowledgement requested, Non-Profit | biotools:rna-express, OMICS_01285 | https://bio.tools/rna-express | SCR_005167 | 2026-02-14 02:01:04 | 5 |
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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 2U24DK097771-09.
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