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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DiProGB Resource Report Resource Website 1+ mentions |
DiProGB (RRID:SCR_005651) | DiProGB | software resource | Genome browser that encodes the genome sequence by physico-chemical dinucleotide properties such as stacking energy, melting temperature or twist angle. Analyses can be performed for the + and ?, as well as for the double strand. | genome, browser, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: Dinucleotide Property Database |
PMID:19605418 | Free, Freely available | biotools:diprogb, OMICS_00880 | https://bio.tools/diprogb | SCR_005651 | DiProGB - The Dinucleotide Properties Genome Browser, Dinucleotide Properties Genome Browser | 2026-02-14 02:00:58 | 4 | |||||
|
Bismark Resource Report Resource Website 1000+ mentions |
Bismark (RRID:SCR_005604) | Bismark | software resource | Software tool to map bisulfite converted sequence reads and determine cytosine methylation states. Flexible aligner and methylation caller for Bisulfite-Seq applications. Used to map bisulfite treated sequencing reads to genome of interest and perform methylation calls in single step. | Map bisulfite treated sequence reads, determine cytosine methylation states, genome, sequence reads, perform methylation calls, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Babraham Institute |
PMID:21493656 DOI:10.1093/bioinformatics/btr167 |
Free, Available for download, Freely available | biotools:bismark, OMICS_00575 | https://github.com/FelixKrueger/Bismark https://bio.tools/bismark |
https://sources.debian.org/src/bismark/ | SCR_005604 | 2026-02-14 02:01:09 | 1123 | |||||
|
Staden Package Resource Report Resource Website 50+ mentions |
Staden Package (RRID:SCR_005629) | software resource | A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows. | c, unix/linux, sequence assembly, dna/protein analysis, spin, sequence alignment, genome, genome viewer, c++, fortran, tcl, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20513662 DOI:10.1093/bioinformatics/btq268 |
BSD License | OMICS_00894, biotools:staden | https://bio.tools/staden https://sources.debian.org/src/staden/ |
SCR_005629 | Staden Package | 2026-02-14 02:01:09 | 79 | ||||||
|
EBCall Resource Report Resource Website 10+ mentions |
EBCall (RRID:SCR_006791) | EBCall | software resource | A software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies. | mutation, cancer, genome, sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tokyo; Tokyo; Japan |
PMID:23471004 | Copyright conditions, Acknowledgement required | biotools:ebcall, OMICS_00084 | https://bio.tools/ebcall | SCR_006791 | EBCall (Empirical Baysian mutation Calling), Empirical Baysian mutation Calling | 2026-02-14 02:01:23 | 19 | |||||
|
Genome Research Foundation Resource Report Resource Website 1+ mentions |
Genome Research Foundation (RRID:SCR_006056) | GRF, GF | institution | The Genome Foundation (AKA Genome Research Foundation) is a fully government accredited and registered non-profit research foundation. GRF aims to provide genome philosophy, science, and technology. GRF is a nonprofit publisher, and research and advocacy organization to promote completely free publication of knowledge with minimum restriction. Our core objectives are to: * Provide ways to overcome unnecessary barriers to immediate availability, access, and use of research * Pursue a publishing strategy that optimizes the openness, quality, and integrity of the publication process * Develop innovative approaches to the assessment, organization, and reuse of ideas and data Genome Foundation Research * Personalized Medicine * Personal Genomics * AngioGenesis drug * Bioinformatics * RNA expression * Protein structure * Human Genome Rights Projects at Genome Foundation * The Human Genome Rights * Human Genome Rights Petition * Free Personal Genome Sequencing Project * Free Personal Genome Sequencing Petition * Tiger Genome Initiative: Amur Tiger and big cat genomes * Whale Genome Project | bioinformatics, genomics, genome, genome sequencing, personalized medicine, personal genomics, angiogenesis, drug, rna expression, protein structure |
has parent organization: Korean Ministry of Education Science and Technology is parent organization of: MetaBase |
Content is available under BioLicense: the freest license. | grid.410888.d, nlx_151458, Wikidata: Q5533483 | https://ror.org/03khjyh83 | SCR_006056 | Genome Foundation | 2026-02-14 02:01:02 | 1 | ||||||
|
estMOI Resource Report Resource Website 10+ mentions |
estMOI (RRID:SCR_006192) | estMOI | software resource | A per-based software to estimate multiplicity of infection (MOI) in parasite genomic sequence data. It is primarily developed to address the limitations of current laboratory (PCR) based estimates of multiplicity using high throughput sequence data. It requires a BAM (alignment output of short reads to the reference genome), VCF (a file with information on variant calls) and FASTA (reference genome) files. # Short reads are aligned to a reference genome using BWA, BOWTIE, SMALT or other short read aligners to generate a BAM file. # Single Nucleotide Polymorphisms (SNPs) are then identified using SAMTools/BCFtools and stored in the VCF format. # The reference FASTA file is expected to be indexed using ''samtools faidx'' to generate a *.fai file. estMOI generates files containing MOI estimates for each SNP combinations (file with name *.log) and a summary for all chromosomes (file with name *.txt). | multiplicity of infection, parasite, genome, high throughput sequencing, single nucleotide polymorphism, chromosome | is listed by: OMICtools | PMID:24443379 | Free, Public | OMICS_02240 | SCR_006192 | estMOI - Estimating multiplicity of infection using parasite deep sequencing data | 2026-02-14 02:01:14 | 10 | ||||||
|
ESTHER Resource Report Resource Website 100+ mentions |
ESTHER (RRID:SCR_002621) | ESTHER | data or information resource, database | Database and tools for analysis of protein and nucleic acid sequences belonging to superfamily of alpha/beta hydrolases homologous to cholinesterases. Covers multiple species, including human, mouse caenorhabditis and drosophila., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | alpha hydrolase, beta hydrolase, cholinesterase, protein, protein superfamily, blast, gene, protein binding, protein-protein interaction, nucleotide, nucleotide sequence, enzyme, genetics, genome, genomics, mutation, disease, gene expression, peptide, chromosome |
is listed by: re3data.org is related to: UniProtKB is related to: AceDB has parent organization: INRA - French National Institute for Agricultural Research; Paris; France |
PMID:23193256 | Free, Available for download, Freely available | nif-0000-30526, SCR_008479, nif-0000-02817, r3d100010542 | https://doi.org/10.17616/R33K77 | SCR_002621 | ESTerases and alpha/beta-Hydrolase Enzymes and Relatives, ESTHER Database, ESTerases and alpha / beta-hydrolase Enzymes and Relatives | 2026-02-14 02:00:18 | 134 | |||||
|
PennCNV Resource Report Resource Website 100+ mentions |
PennCNV (RRID:SCR_002518) | PennCNV | software resource | A free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays. PennCNV implements a hidden Markov model (HMM) that integrates multiple sources of information to infer CNV calls for individual genotyped samples. It differs form segmentation-based algorithm in that it considered SNP allelic ratio distribution as well as other factors, in addition to signal intensity alone. In addition, PennCNV can optionally utilize family information to generate family-based CNV calls by several different algorithms. Furthermore, PennCNV can generate CNV calls given a specific set of candidate CNV regions, through a validation-calling algorithm. | imaging genomics, copy number variation, snp, genotyping array, array, oligonucleotide, hidden markov model, genotype, genome |
is listed by: OMICtools is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: VegaMC is related to: OpenBioinformatics.org has parent organization: University of Pennsylvania; Philadelphia; USA |
NIMH MH604687 | PMID:17921354 | Free | OMICS_00729, nlx_155921 | http://www.openbioinformatics.org/penncnv/ |
http://www.neurogenome.org/cnv/penncnv | SCR_002518 | PennCNV: copy number variation detection | 2026-02-14 02:00:26 | 349 | |||
|
FlyMine Resource Report Resource Website 100+ mentions |
FlyMine (RRID:SCR_002694) | FlyMine | data or information resource, database | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. Integrated database of genomic, expression and protein data for Drosophila, Anopheles, C. elegans and other organisms. You can run flexible queries, export results and analyze lists of data. FlyMine presents data in categories, with each providing information on a particular type of data (for example Gene Expression or Protein Interactions). Template queries, as well as the QueryBuilder itself, allow you to perform searches that span data from more than one category. Advanced users can use a flexible query interface to construct their own data mining queries across the multiple integrated data sources, to modify existing template queries or to create your own template queries. Access our FlyMine data via our Application Programming Interface (API). We provide client libraries in the following languages: Perl, Python, Ruby and & Java API | anopheles, genome, c. elegans, drosophila, gene, chromosomal location, genomics, proteomics, gene expression, interaction, homology, function, regulation, protein, phenotype, pathway, disease, publication, FASEB list |
is related to: FlyBase is related to: UniProt is related to: Ensembl is related to: InterPro is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is related to: Tree families database is related to: IntAct is related to: Gene Ontology is related to: GOA is related to: ArrayExpress is related to: REDfly Regulatory Element Database for Drosophilia is related to: KEGG is related to: Reactome has parent organization: University of Cambridge; Cambridge; United Kingdom |
Wellcome Trust 067205; NHGRI |
PMID:17615057 | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-02845 | SCR_002694 | 2026-02-14 02:00:26 | 104 | ||||||
|
Biomol-Informatics Resource Report Resource Website 1+ mentions |
Biomol-Informatics (RRID:SCR_004081) | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 12, 2021. Technology based company in Madrid that offers consulting services on Bioinformatics in areas of research, diagnostics and pharmaceutical industry. | bioinformatics, genome sequencing, genome, sequencing, exome, protein-protein interaction, analysis, molecular dynamics, 3d modeling, evolutive information, training service resource, next generation sequencing, simulation, drug design, computational simulation, macromolecule, molecular dynamics, quantum mechanics, molecular mechanics, dna, protein |
is related to: European Gram Negative AntiBacterial Engine has parent organization: Autonomous University of Madrid; Madrid; Spain |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_158539, grid.432020.7, Wikidata Q30254873 | https://ror.org/057rd1163 | SCR_004081 | Biomol-Informatics SL | 2026-02-14 02:00:56 | 3 | |||||||
|
MSG Resource Report Resource Website 1+ mentions |
MSG (RRID:SCR_004161) | MSG | software resource | A pipeline of scripts to assign ancestry to genomic segments using next-gen sequence data. This method can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations. | next generation sequencing, genotyping, genetic mapping, ancestry, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
PMID:21233398 | OMICS_01551 | SCR_004161 | Multiplexed shotgun genotyping, Multiplexed shotgun genotyping (MSG), MSG: Multiplexed Shotgun Genotyping | 2026-02-14 02:00:41 | 2 | |||||||
|
PerM Resource Report Resource Website 50+ mentions |
PerM (RRID:SCR_004223) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. | Short sequencing mapping, short sequencing read, next-generation sequencing, genome, alignment, short read, abi, solid, illumina, , bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Clippers has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:19675096 DOI:10.1093/bioinformatics/btp486 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00675, biotools:perm | https://bio.tools/perm https://sources.debian.org/src/perm/ |
SCR_004223 | PERiodic seed Mapping, Periodic seed Mapping | 2026-02-14 02:00:38 | 60 | ||||||
|
NovelSeq Resource Report Resource Website |
NovelSeq (RRID:SCR_003136) | NovelSeq | software resource | Software pipeline to detect novel sequence insertions using high throughput paired-end whole genome sequencing data. | sequence, insertion, genome sequencing, genome, next-generation sequencing, illumina, unix, linux, c, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: SourceForge |
PMID:20385726 | Free, Available for download, Freely available | biotools:novelseq, nlx_156791, OMICS_02164 | https://mybiosoftware.com/novelseq-1-0-2-sequence-insertions-detection.html#google_vignette | SCR_003136 | NovelSeq: Novel Sequence Insertion Detection | 2026-02-14 02:00:30 | 0 | |||||
|
mrCaNaVaR Resource Report Resource Website 10+ mentions |
mrCaNaVaR (RRID:SCR_003135) | mrCaNaVaR | software resource | Copy number caller that analyzes the whole-genome next-generation sequence mapping read depth to discover large segmental duplications and deletions. It also has the capability of predicting absolute copy numbers of genomic intervals. | genome, next-generation sequence, duplication, deletion, copy number variant, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: SPLITREAD has parent organization: SourceForge |
Free, Freely available | OMICS_02138, nlx_156790, biotools:mrcanavar | https://bio.tools/mrcanavar | SCR_003135 | mrCaNaVaR - micro-read Copy Number Variant Regions, micro-read Copy Number Variant Regions | 2026-02-14 02:00:40 | 14 | ||||||
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deCODE genetics Resource Report Resource Website 50+ mentions |
deCODE genetics (RRID:SCR_003334) | deCODE | commercial organization | A biopharmaceutical company applying its discoveries in human genetics to develop drugs and diagnostics for common diseases. They specialize in gene discovery - their population approach and resources have enabled them to isolate key genes contributing to major public health challenges from cardiovascular disease to cancer. The company's genotyping capacity is now one of the highest in the world. They have a large population-based biobank containing whole blood and DNA samples with extensive relevant phenotypic information from around 120.000 Icelanders. In the company's work in more than 50 disease projects, their statistical and informatics departments have established themselves in data processing and analysis. deCODE genetics is widely recognized as a center of excellence in genetic research. | biopharmaceutical, genetics, drug, diagnostic, genotyping, phenotype, data processing, analysis, genetic variant, risk factor, genome, blood, dna, biobank, single nucleotide polymorphism |
is related to: EU-AIMS is related to: NEWMEDS |
Schizophrenia, Cardiovascular disease, Cancer, Type 2 diabetes, Atrial fibrillation, Heart attack | Free, Freely available | nif-0000-31959, ISNI: 0000 0004 0618 6889, grid.421812.c, Wikidata: Q493712 | https://ror.org/04dzdm737 | SCR_003334 | Islensk Erfdagreining EHF, Islensk Erfdagreining | 2026-02-14 02:00:46 | 57 | |||||
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Parseq Resource Report Resource Website 1+ mentions |
Parseq (RRID:SCR_003464) | Parseq | software resource | Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders. | rna-seq, genome, transcription, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Sorbonne University; Paris; France |
PMID:24470570 | Free, Available for download, Freely available | biotools:parseq, OMICS_02302 | https://bio.tools/parseq | SCR_003464 | 2026-02-14 02:00:49 | 2 | ||||||
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EdgeBio Resource Report Resource Website |
EdgeBio (RRID:SCR_000183) | EdgeBio | commercial organization | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A contract research organization that provides genomics services such as sequencing, bioinformatics, NGS data analysis and whole exome sequencing. EdgeBio is a CLIA-approved service provider. | contract research organization, CRO, genomics, genome, sequencing, bioinformatics, NGS data analysis, whole exome sequencing, research, Illumina NGS | is listed by: ScienceExchange | THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_203 | https://www.edgebio.com/ | SCR_000183 | Edge Bio, EdgeBio.com | 2026-02-14 01:59:38 | 0 | ||||||
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ARACHNE Resource Report Resource Website 1+ mentions |
ARACHNE (RRID:SCR_000351) | ARACHNE | software resource | A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads. | genome, sequencing, analysis, sanger, chemistry, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Broad Institute |
PMID:11779843 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01812, biotools:arachne | https://bio.tools/arachne | SCR_000351 | ARACHNE: a whole-genome shotgun assembler, ARACHNE (Unsupported) | 2026-02-14 01:59:42 | 3 | |||||
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HudsonAlpha Genomics Services Lab Resource Report Resource Website |
HudsonAlpha Genomics Services Lab (RRID:SCR_000353) | HudsonAlpha Genomics Services Lab | service resource | A lab that offers genetic research tools such as RNA sequencing and a variety of arrays. | genome, sequencing, assembly, rna, microarray, exome | is listed by: ScienceExchange | THIS RESOURCE IS NO LONGER IN SERVICE | SciEx_221 | SCR_000353 | HudsonAlpha Institute for Biotechnology Genomics Services Lab, Genomics Services Lab | 2026-02-14 01:59:42 | 0 | |||||||
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Pindel Resource Report Resource Website 10+ mentions |
Pindel (RRID:SCR_000560) | Pindel | software resource | Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | deletion, insertion, nucleotide, genome, read, inversion, tandem duplication, structural variant, next-generation sequencing, pattern growth, indel, breakpoint, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA works with: cgpPindel |
PMID:19561018 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:pindel, OMICS_00321 | https://bio.tools/pindel | SCR_000560 | 2026-02-14 01:59:46 | 22 |
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