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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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nsSNPAnalyzer Resource Report Resource Website 50+ mentions |
nsSNPAnalyzer (RRID:SCR_010780) | nsSNPAnalyzer | analysis service resource, data analysis service, data analysis software, data processing software, production service resource, service resource, software application, software resource | A tool to predict whether a nonsynonymous single nucleotide polymorphism (nsSNP) has a phenotypic effect. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Tennessee Health Science Center; Tennessee; USA |
OMICS_00156, biotools:nssnpanalyzer | https://bio.tools/nssnpanalyzer | SCR_010780 | nsSNPAnalyzer: predicting disease-associated nonsynonymous single nucleotide polymorphisms | 2026-09-05 06:26:46 | 50 | |||||||
|
PhD-SNP Resource Report Resource Website 100+ mentions |
PhD-SNP (RRID:SCR_010782) | PhD-SNP | software resource | It is based a SVM-based classifier. | is listed by: OMICtools | PMID:16895930 | OMICS_00158 | SCR_010782 | Predictor of human Deleterious Single Nucleotide Polymorphisms | 2026-09-05 06:26:46 | 335 | ||||||||
|
PMut Resource Report Resource Website 50+ mentions |
PMut (RRID:SCR_010783) | PMut | software resource | A software aimed at the annotation and prediction of pathological mutations. | is listed by: OMICtools | PMID:15390262 | OMICS_00159 | SCR_010783 | 2026-09-05 06:26:46 | 80 | |||||||||
|
Medical Biobank Resource Report Resource Website |
Medical Biobank (RRID:SCR_010748) | Medical Biobank | biospecimen repository, material storage repository, service resource, storage service resource | A biobank created from a cross-sectional population of a town in Sweden. The Medical Biobank is mainly based on three cohorts: The V��sterbotten intervention cohort, the MONICA-cohort, and the Mammary screening cohort. These sub-cohorts together are named Northern Sweden Health and Disease Study Cohort (North Health). These sub-cohorts together is named Northern Sweden Health and Disease Study Cohort (North Health). Originally, the V��sterbotten Intervention program (VIP) is a long-term project intended for health promotion of the population of V��sterbotten. All individuals 40, 50 and 60 years of age in the population of the county are invited for screening (approx. 254.000 inhabitants). They are asked to complete a questionnaire concerning various lifestyle factors including diet. They are also asked to donate a separate blood sample to the Medical Biobank for freeze storage for later research purposes. The project started in 1985 and the cohort covered in December 2002, 74,000 individuals, of whom 67,000 had donated blood samples. The material is supplemented with population based samples from a local mammary screening (44,000 sampling occasions, 25,700 unique individuals) and from the Northern Sweden MONICA Project (11,500 sampling occasions, 7,500 unique individuals). The total cohort contains at the moment 85.000 unique individuals with 130.000 sampling occasions. The VIP and MONICA cohorts are population based and the mammary screening cohort are nearly population based. Follow-up: * For the VIP-cohort a second sample (and questionnaire) is collected with a 10-year interval of the individuals within the cohort. * Repeated sampling was performed in the MONICA project in 1999 on individuals participating in 1986, 1990, and 1994. * From 1997 repeated screening has started within the mammary screening program with sampling every second year, in the age group 50-69 years within the county. Biobank content: * Life-Style Questionnaire: Every attending subject is asked to answer a questionnaire, which in the VIP and MONICA-projects includes questions about education, occupation/working conditions, daily habits including smoking, diet, etc and in the mammary screening cohort on reproductive conditions. The dietary questionnaire has been validated twice. The data from the questionnaires, as well as from results from the biobank, are kept in a database for future research purposes. The questionnaires in the VIP and the MONICA project are optically read. * Measurements: Blood Pressure, Anthropometry, Glucose Tolerance Test, Blood Lipids * Blood Samples: The attendants are asked for their willingness to donate a sample of 20-ml whole blood for future analyses. The sample is taken after 4 hours of fasting or in the morning after an over night fasting (most samples) in the VIP and MONICA cohorts. The 20-ml sample is divided into 10 subsamples consisting of 6 plasma, 2 leukocyte (buffy coat) and 2 erythrocyte samples. All material is frozen at -80 degrees C. The organization of the bank is elaborated with specially trained staff and an organization of transport-, storage- and security facilities. For DNA handling a specialized laboratory has been built up. * End-points: Mortality, Cancer events, Cardiovascular events, Other morbidity, Other registry-based follow-up * Registries: At regular intervals the cohort is scanned for incident myocardial infarctions (MI) and stroke utilizing the Northern Sweden MONICA registry and for cancer using the regional cancer registry. In the future the same procedure will be applied also on other registries e.g. diabetes, osteoporosis, dementia. | lifestyle, diet, adult, questionnaire |
is listed by: One Mind Biospecimen Bank Listing is related to: Swedish National Biobank Program has parent organization: Umea University; Umea; Sweden |
General adult population, (40 50 and 60 years of age), Adult, Middle adult human, Aging | Public: The Medical Biobank has been positioned as a national and international resource for scientific research. All applications must be: Approved by the Board of Experts, Research Ethics Committee and Medical Biobank. | nlx_99793 | SCR_010748 | Biobank of Northern Sweden | 2026-09-05 06:26:45 | 0 | ||||||
|
Integra Life Sciences Resource Report Resource Website 100+ mentions |
Integra Life Sciences (RRID:SCR_010741) | commercial organization | Commercial tissue bank for human tissues. | life science, organization, commercial, surgical instrument, neurosurgery | Commercial | grid.481865.6, nlx_97702 | https://ror.org/04t8qhn97 | SCR_010741 | Integra | 2026-09-05 06:26:45 | 385 | ||||||||
|
ALLPATHS-LG Resource Report Resource Website 100+ mentions |
ALLPATHS-LG (RRID:SCR_010742) | ALLPATHS-LG | software resource | Software tool as whole genome shotgun assembler that can generate high quality genome assemblies using short reads (~100bp) such as those produced by the new generation of sequencers. | genome assembly, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Broad Institute |
PMID:21187386 | OMICS_00007, biotools:allpaths-lg | https://bio.tools/allpaths-lg | SCR_010742 | 2026-09-05 06:26:45 | 237 | |||||||
|
Celera assembler Resource Report Resource Website 50+ mentions |
Celera assembler (RRID:SCR_010750) | Celera assembler | software resource | A de novo whole-genome shotgun (WGS) DNA sequence assembler. |
is listed by: OMICtools is related to: Canu has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00009 | SCR_010750 | 2026-09-05 06:26:45 | 59 | |||||||||
|
SOAPdenovo Resource Report Resource Website 1000+ mentions |
SOAPdenovo (RRID:SCR_010752) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 24,2023. Software tool for de novo assembly of human genomes with massively parallel short read sequencing.Short-read assembly method that can build de novo draft assembly for human sized genomes.Software package for assembling short oligonucleotide into contigs and scaffolds., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, rna, dna, de novo, genome assembly, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:20019144 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00031, biotools:soapdenovo, SCR_014986 | https://github.com/aquaskyline/SOAPdenovo2, https://bio.tools/soapdenovo, https://sources.debian.org/src/soapdenovo/, | SCR_010752 | SOAPdenovo2 | 2026-09-05 06:26:45 | 1342 | ||||||
|
SUTTA Resource Report Resource Website |
SUTTA (RRID:SCR_010754) | SUTTA | software resource | A new De Novo DNA sequence assembler based on global search-methods in order to contain the complexity of the assembly problem. | is listed by: OMICtools | OMICS_00034 | SCR_010754 | 2026-09-05 06:26:45 | 0 | ||||||||||
|
Velvet Resource Report Resource Website 1000+ mentions |
Velvet (RRID:SCR_010755) | Velvet | data analysis software, data processing software, sequence analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package as de novo genomic assembler for short read sequencing technologies using de Bruijn graphs. Takes in short read sequences, removes errors, then produces high quality unique contigs, retrieves repeated areas between contigs. Can leverage very short reads in combination with read pairs to produce useful assemblies. Operating system Unix/Linux., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | de novo, genomic, assembly, short, read, sequencing, de Bruijn, graph, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Velvet-SC is related to: shovill has parent organization: European Bioinformatics Institute |
EMBL | PMID:18349386 DOI:10.1101/gr.074492.107 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00038, biotools:velvet | https://www.ebi.ac.uk/~zerbino/velvet/, https://bio.tools/velvet, https://sources.debian.org/src/velvet/ | SCR_010755 | 2026-09-05 06:26:46 | 1039 | |||||
|
Atlas2 Resource Report Resource Website 10+ mentions |
Atlas2 (RRID:SCR_010756) | software resource | A next-generation sequencing suite of variant analysis tools specializing in the separation of true SNPs and insertions and deletions (indels) from sequencing and mapping errors in WECS data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Baylor University; Texas; USA |
PMID:22239737 | biotools:atlas_suite, OMICS_00051 | https://bio.tools/atlas_suite | SCR_010756 | Atlas Suite | 2026-09-05 06:26:46 | 11 | |||||||
|
FamSeq Resource Report Resource Website |
FamSeq (RRID:SCR_010760) | FamSeq | software resource | A computational tool for calculating probability of variants in family-based sequencing data. | c++ |
is listed by: OMICtools has parent organization: University of Texas MD Anderson Cancer Center |
PMID:23426633 | OMICS_00058 | SCR_010760 | Family-Based Sequencing Program | 2026-09-05 06:26:46 | 0 | |||||||
|
GenePix Pro Resource Report Resource Website 500+ mentions |
GenePix Pro (RRID:SCR_010969) | GenePix Pro | software resource | Industry standard microarray image analysis software because of its unique combination of imaging and analysis tools, visualizations, automation capabilities, performance and intuitive workflows. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_00840 | SCR_010969 | 2026-09-05 06:26:51 | 634 | ||||||||||
|
OligoArray Resource Report Resource Website 10+ mentions |
OligoArray (RRID:SCR_010961) | OligoArray | software resource | A free software that computes gene specific oligonucleotides for genome-scale oligonucleotide microarray construction. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Michigan; Ann Arbor; USA |
PMID:12799432 | OMICS_00828, biotools:oligoarray | https://bio.tools/oligoarray | SCR_010961 | OligoArray 2.0: Design of oligonucleotide probes for DNA microarrays using a thermodynamic approach, OligoArray 2.1: Genome-scale oligonucleotide design for microarrays | 2026-09-05 06:26:51 | 38 | ||||||
|
Picky Resource Report Resource Website 10+ mentions |
Picky (RRID:SCR_010963) | Picky | software resource | A software tool for selecting optimal oligonucleotides (oligos) that allows the rapid and efficient determination of gene-specific oligos based on given gene sets, and can be used for large, complex genomes such as human, mouse, or maize. |
is listed by: OMICtools has parent organization: Iowa State University; Iowa; USA |
NSF DBI0850195 | PMID:15180932 PMID:19849862 PMID:20406469 |
Free, Public, Acknowledgement requested | OMICS_00833 | SCR_010963 | Picky: Optimal Oligonucleotide Design and Analysis | 2026-09-05 06:26:51 | 39 | ||||||
|
ROSO Resource Report Resource Website 1+ mentions |
ROSO (RRID:SCR_010967) | ROSO | software resource | A software to design optimized oligonucleotide probes (size over 25 nucleotides) for microarrays. |
is listed by: OMICtools has parent organization: PRABI |
PMID:14734320 | Free to non-profit users, On request | OMICS_00838 | SCR_010967 | ROSO - A friend for your design, Recherche et Optimisation de Sondes Oligonucl��otidiques, Recherche et Optimisation de Sondes Oligonucleotidiques | 2026-09-05 06:26:51 | 1 | |||||||
|
Array Studio Resource Report Resource Website 1+ mentions |
Array Studio (RRID:SCR_010970) | analysis service resource, data analysis software, data processing software, production service resource, service resource, software application, software resource, software toolkit | Software package which provides statistics and visualization for analysis of high dimensional quantification data including microarray or RTPCR data or Taqman data, genotype data including SNP or Copy Number data and Next Generation Sequencing data. Provides integrated environment for analyzing and visualizing high dimensional data. | Statistic, visualization, data, analysis, quantification, integrated environment, microarray data, RTPCR data, Taqman data, genotype data, copy number data, next generation sequencing data | Free, Available for download, Freely available | OMICS_00850 | https://omicsoftdocs.github.io/ArraySuiteDoc/tutorials/ArrayStudio/ArrayStudio/ | http://www.omicsoft.com/array-studio.php | SCR_010970 | 2026-09-05 06:26:51 | 5 | ||||||||
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UNC Microarray Database Resource Report Resource Website 10+ mentions |
UNC Microarray Database (RRID:SCR_010979) | UNC MD, UNCMD | data or information resource, data repository, database, service resource, storage service resource | Database for microarray data storage, retrieval, analysis, and visualization. | microarray, FASEB list |
is listed by: OMICtools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
Account required, The community can contribute to this resource | OMICS_00872 | SCR_010979 | UNC-Chapel Hill Microarray Database | 2026-09-05 06:26:51 | 33 | |||||||
|
GenomeStudio Resource Report Resource Website 1000+ mentions |
GenomeStudio (RRID:SCR_010973) | GenomeStudio | software resource | Visualize and analyze data generated by all of Illumina''s platforms. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_00854 | SCR_010973 | 2026-09-05 06:26:51 | 3057 | ||||||||||
|
ComBat Resource Report Resource Website 1000+ mentions |
ComBat (RRID:SCR_010974) | ComBat | software resource | Adjusting batch effects in microarray expression data using Empirical Bayes methods. |
is listed by: OMICtools is listed by: SoftCite |
OMICS_00857 | SCR_010974 | 2026-09-05 06:26:51 | 3983 |
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The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
