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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DETONATE Resource Report Resource Website 1+ mentions |
DETONATE (RRID:SCR_017035) | DETONATE | software application, sequence analysis software, data processing software, software resource, data analysis software | Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences. | evaluate, de novo, transcriptome, assembly, RNAseq, data, RSEM-EVAL, REF-EVAL, dataset, genomic, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NHGRI R01 HG005232; NLM T15 LM007359 |
PMID:25608678 | Free, Available for download, Freely available | biotools:detonate | https://bio.tools/detonate | SCR_017035 | DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation, DETONATE | 2026-02-15 09:21:57 | 2 | ||||
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RepeatFiller Resource Report Resource Website 10+ mentions |
RepeatFiller (RRID:SCR_017414) | software application, data processing software, software resource, alignment software, image analysis software | Software tool to incorporate newly detected repeat overlapping alignments into pairwise alignment chains. It only aligns local genomic regions that are bounded by colinear aligning blocks, as provided in chains, which makes it feasible to consider all seeds including those that overlap repetitive regions. Used to improve genome alignments by incorporating previously undetected local alignments between repetitive sequences. | Repeat, overlapping, alignment, pairwise, chain, local, genomic, region, colinear, block, sequence, undetected, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany |
DOI:10.1101/696922 | Free, Freely available | biotools:RepeatFiller, BioTools:RepeatFiller | https://bio.tools/RepeatFiller https://bio.tools/RepeatFiller https://bio.tools/RepeatFiller |
SCR_017414 | 2026-02-15 09:22:02 | 15 | |||||||
|
GCE Resource Report Resource Website 10+ mentions |
GCE (RRID:SCR_017332) | software application, data processing software, data analysis software, software resource | Software tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics. | estimation, genomic, characteristic, analysis, k-mer, frequencey, de novo | ftp://ftp.genomics.org.cn/pub/gce | SCR_017332 | Genomic Characteristics Estimation | 2026-02-15 09:22:03 | 14 | ||||||||||
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4D Genome Resource Report Resource Website 10+ mentions |
4D Genome (RRID:SCR_017489) | database, service resource, storage service resource, data repository, data or information resource | Repository for chromatin interaction data. Records can be queried by genomic regions, gene names, organism, and detection technology. Database is continuously updated by curators. Contributions from scientific community. | Repository, chromatic, interaction, data, genomic, region, gene, name, detection, technology, curated | has parent organization: University of Pennsylvania; Philadelphia; USA | Free, Available for download, Freely available | r3d100012282 | https://doi.org/10.17616/R3SH37 | SCR_017489 | 2026-02-15 09:21:21 | 10 | ||||||||
|
AmoebaDB Resource Report Resource Website 1+ mentions |
AmoebaDB (RRID:SCR_017592) | database, service resource, production service resource, data or information resource, analysis service resource | Integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. Contains genomes of three Entamoeba species and microarray expression data for E. histolytica. Integrates whole genome sequence and annotation and includes experimental data and environmental isolate sequences provided by community researchers. | Genomic, functional, database, Entamoeba, Acanthamoeba, parasite, microarray, expression, data, experimental, isolate, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Eukaryotic Pathogen Database Resources |
NIDA ; Department of Health and Human Services ; NIH |
PMID:20974635 | Free, Freely available | biotools:amoebadb, r3d100012457 | https://bio.tools/amoebadb https://doi.org/10.17616/R3PX9Q |
SCR_017592 | 2026-02-15 09:22:09 | 7 | ||||||
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CoronaVIR Resource Report Resource Website 1+ mentions |
CoronaVIR (RRID:SCR_018338) | disease-related portal, topical portal, data or information resource, portal | Web based platform on COVID-19 to maintain predicted diagnostic, drug and vaccine candidates and computational resources on novel coronavirus SARS-CoV-2 and its resulting disease COVID-19. Provides collected and organized information from literature and other resources from internet, links to appropriate literature . Integrated multi-omics repository dedicated to current genomic, proteomic, diagnostic and therapeutic knowledge about coronaviruses. | COVID-19, SARS-CoV-2, diagnostic, drug, candidate, computational resource. coronavirus, disease, literature, genomic, proteomic, data | COVID-19 | DOI:10.31219/osf.io/xegzu | Free, Freely available | SCR_018351 | SCR_018338 | 2026-02-15 09:21:36 | 4 | ||||||||
|
Conrad Prebys Center for Chemical Genomics Resource Report Resource Website |
Conrad Prebys Center for Chemical Genomics (RRID:SCR_001687) | organization portal, data or information resource, portal | The Conrad Prebys Center for Chemical Genomics (CPCCG) uses advanced screening technologies to identify high level chemical probes that interact with proteins involved in cellular processes. Optimization of these probes using medicinal chemistry and informatics will form the basis of a new generation of medicines. CPCCG is 1 of 4 Comprehensive Centers chosen nationally to be a part of the Molecular Libraries Probe Program (MLP), which established the Molecular Libraries Probe Production Centers Network (MLPCN). The goal is to produce small molecule probes that allow research into health and disease on the cellular level. CPCCG core services span a range of biochemical and cell-based screens for obtaining hits and provide chemistry resources for optimizing hits into probes or drug development. - Full scale screening capabilities and technology which can provide rapid screening on a broad diversity of assays and detection platforms - Several fully-integrated industrial-scale high-throughput screening (HTS) workstations - HTS microscopy/HCS and novel algorithm development for image analysis - Full hit-to-probe chemistry and exploratory pharmacology - Powerful NMR based Chemical Fragment Screening - Highly integrated informatics infrastructure and efficient data mining capabilities - Protein production facility - Cell production facility for scale-up tissue culture The CPCCG Screening Core can screen 96, 384 or 1536 well formats using either biochemical or cell-based assays, and can process over 300,000 wells per day. Total throughput capacity will climb to over 2 million compounds per day following the opening of Burnhams east coast campus in Lake Nona, Florida. | drug, algorithm, analysis, assay, biochemical, cell, cellular, chemical, culture, development, disease, genomic, hcs, health, hts microscopy, keywords: chemical, medicinal, microscopy, molecular, molecule, probe, process, production, protein, technology, tissue, image | Free, Freely Available | nif-0000-10180 | http://sdccg.burnham.org | SCR_001687 | CPCCG | 2026-02-15 09:18:09 | 0 | ||||||||
|
SOAP Resource Report Resource Website 100+ mentions |
SOAP (RRID:SCR_000689) | SOAP, | software application, data processing software, software resource | Software package that provides full solution to next generation sequencing data analysis consisting of an alignment tool (SOAPaligner/soap2), a re-sequencing consensus sequence builder (SOAPsnp), an indel finder ( SOAPindel ), a structural variation scanner ( SOAPsv ), a de novo short reads assembler ( SOAPdenovo ), and a GPU-accelerated alignment tool for aligning short reads with a reference sequence. (SOAP3/GPU)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, next generation sequencing, alignment, short read, bio.tools |
lists: SOAPfusion lists: SOAPfuse lists: SOAPnuke lists: GapCloser is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian has parent organization: BGI; Shenzhen; China is parent organization of: SOAP3 is parent organization of: SOAPaligner/soap2 |
PMID:18227114 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154652, biotools:soap | https://bio.tools/soap | SCR_000689 | SOAP: short oligonucleotide alignment program, Short Oligonucleotide Analysis Package | 2026-02-15 09:17:58 | 402 | |||||
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HAPLO 2 Resource Report Resource Website 1+ mentions |
HAPLO 2 (RRID:SCR_009059) | HAPLO 2 | software application, software resource | Software application that estimates frequencies of multi-site haplotypes using the EM algorithm (entry from Genetic Analysis Software) | gene, genetic, genomic, fortran, dec vax | is listed by: Genetic Analysis Software | nlx_154040 | SCR_009059 | 2026-02-15 09:19:56 | 1 | |||||||||
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UNPHASED Resource Report Resource Website 100+ mentions |
UNPHASED (RRID:SCR_009056) | UNPHASED | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. A suite of programs for association analysis of multilocus haplotypes from unphased genotype data. These include TDTPHASE for case-parent trios, COCAPHASE for case/control data, QTPHASE for quantitative traits in unrelateds, PDTPHASE for general pedigrees, and QPDTPHASE for quantitative traits in general pedigrees. Features include global and individual haplotype tests, main effects and conditional tests, grouping of rare haplotypes, pairwise comparisons of haplotype risk, flexible permutation procedures and calculation of LD measures. | gene, genetic, genomic, c++, java, unix, solaris, linux, ms-windows | is listed by: Genetic Analysis Software | PMID:10739137 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154037 | http://www.mrc-bsu.cam.ac.uk/personal/frank/software/unphased/ | SCR_009056 | 2026-02-15 09:19:37 | 125 | ||||||
|
POWER Resource Report Resource Website 500+ mentions |
POWER (RRID:SCR_009057) | POWER | software application, software resource | Windows-based program for computation of sample size and power for binary outcome studies (case-control and cohort studies) based on a logistic-like regression model with one covariate or two covariates (e.g., gene-exposure interactions). (entry from Genetic Analysis Software) | gene, genetic, genomic, ms-window | is listed by: Genetic Analysis Software | nlx_154038 | http://dceg.cancer.gov/POWER/ | SCR_009057 | 2026-02-15 09:20:02 | 584 | ||||||||
|
DHSMAP Resource Report Resource Website 1+ mentions |
DHSMAP (RRID:SCR_009160) | DHSMAP | software application, software resource | Software application for fine-mapping of qualitative traits by linkage disequilibrium. Given a set of marker haplotypes or genotypes from affected individuals, haplotypes or genotypes from appropriately selected controls, and a genetic map of the markers at which both sets of individuals are typed, DHSMAP estimates the location of the trait-associated variant by maximum likelihood or maximum quasi-likelihood. (entry from Genetic Analysis Software) | gene, genetic, genomic, c++, unix, solaris, linux | is listed by: Genetic Analysis Software | nlx_154282 | SCR_009160 | Decay of Haplotype Sharing MAPping software | 2026-02-15 09:19:58 | 1 | ||||||||
|
AMELIA Resource Report Resource Website 100+ mentions |
AMELIA (RRID:SCR_009119) | AMELIA | software application, software resource | Software application that employs allele matching to analyse the effects of rare variants within a specific locus. There is increasing evidence that rare variants play a role in some complex traits, but their analysis is not straightforward. Locus-based tests become necessary due to low power in rare variant single-point association analyses. In addition, variant quality scores are available for sequencing data, but are rarely taken into account. To enable this analysis, AMELIA has been developed as an allele-matching approach that is robust to the presence of both directions of effect for variants within the locus analysed. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, unix, linux | is listed by: Genetic Analysis Software | nlx_154222 | SCR_009119 | Allele Matching Empirical Locus-specific Integrated Association test | 2026-02-15 09:19:57 | 121 | ||||||||
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ALLEGRO Resource Report Resource Website 50+ mentions |
ALLEGRO (RRID:SCR_009116) | ALLEGRO | software application, software resource | Software application that is a faster version of GENEHUNTER and Allegro 1.2 (several degrees of increase of speed, can handle bigger families, up to 50 bits) (entry from Genetic Analysis Software) | gene, genetic, genomic, c++ | is listed by: Genetic Analysis Software | nlx_154217 | SCR_009116 | 2026-02-15 09:19:38 | 63 | |||||||||
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SIBSIM Resource Report Resource Website |
SIBSIM (RRID:SCR_009113) | SIBSIM | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. Software application that simulates either genotype and/or quantitative phenotype data in family structures in a modern, easy to use and highly scalable way. It is based on XML, completely written in C++ and published under the GNU General Public License. | gene, genetic, genomic, c++, xml, unix | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154212 | SCR_009113 | 2026-02-15 09:20:03 | 0 | ||||||||
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IGG Resource Report Resource Website 1+ mentions |
IGG (RRID:SCR_009114) | IGG | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVCE, documented September 22, 2016. | gene, genetic, genomic, java, web-based | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154214 | http://bioinfo.hku.hk:13080/iggweb/ | SCR_009114 | Integrate Genotypes for genome-wide Genetic studies | 2026-02-15 09:20:04 | 2 | ||||||
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QTLNETWORK Resource Report Resource Website 50+ mentions |
QTLNETWORK (RRID:SCR_009078) | QTLNETWORK | software application, software resource | Software package for mapping and visualizing the genetic architecture underlying complex traits for experimental populations derived from a cross between two inbred lines. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | PMID:18202029 PMID:20593516 |
nlx_154076 | SCR_009078 | 2026-02-15 09:20:03 | 50 | ||||||||
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TREELD Resource Report Resource Website |
TREELD (RRID:SCR_009111) | TREELD | software application, software resource | Free software tool for mapping complex trait loci. TreeLD performs a multipoint LD-analysis by inferring the ancestry of a genomic region and analyzing this ancestry for signals of disease mutations. The generated likelihoods can be used to test for the presence of a disease locus and to fine-map its location, providing a point estimate and a credible region. Furthermore, the package provides a novel way of visualizing the association signal in a sample. TreeLD is designed for high-density SNP haplotypes and can be applied to case-control data, TDT trio data and quantitative trait data. (entry from Genetic Analysis Software) | gene, genetic, genomic, unix, solaris, linux, ms-windows, (95/98/nt/2000/xp) | is listed by: Genetic Analysis Software | Free | nlx_154210 | SCR_009111 | 2026-02-15 09:19:57 | 0 | ||||||||
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MIXSCORE Resource Report Resource Website 1+ mentions |
MIXSCORE (RRID:SCR_009076) | MIXSCORE | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software application using a method for combining SNP association and admixture association statistics to increase power in GWAS in admixed populations. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154074 | SCR_009076 | 2026-02-15 09:19:37 | 6 | ||||||||
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POWQ Resource Report Resource Website |
POWQ (RRID:SCR_009077) | POWQ | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A user-friendly, graphical package for power evaluation and enhancement planning through variance component linkage analysis in a multipoint framework. (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | PMID:16585065 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154075 | SCR_009077 | 2026-02-15 09:20:02 | 0 |
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