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https://imputationserver.sph.umich.edu/index.html#!pages/home

Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4.

Proper citation: Michigan Imputation Server (RRID:SCR_023554) Copy   

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http://www.scandb.org/newinterface/about.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 17, 2022. A large-scale database of genetics and genomics data associated to a web-interface and a set of methods and algorithms that can be used for mining the data in it. The database contains two categories of single nucleotide polymorphism (SNP) annotations: # Physical-based annotation where SNPs are categorized according to their position relative to genes (intronic, inter-genic, etc.) and according to linkage disequilibrium (LD) patterns (an inter-genic SNP can be annotated to a gene if it is in LD with variation in the gene). # Functional annotation where SNPs are classified according to their effects on expression levels, i.e. whether they are expression quantitative trait loci (eQTLs) for that gene. SCAN can be utilized in several ways including: (i) queries of the SNP and gene databases; (ii) analysis using the attached tools and algorithms; (iii) downloading files with SNP annotation for various GWA platforms. . eQTL files and reported GWAS from NHGRI may be downloaded., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SCAN (RRID:SCR_005185) Copy   

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http://llama.mshri.on.ca/funcassociate/

A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool

Proper citation: FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) Copy   

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https://amp.pharm.mssm.edu/geneshot/

Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations.

Proper citation: Geneshot (RRID:SCR_017582) Copy   

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https://imputationserver.sph.umich.edu/

Web server to implement whole genotype imputation workflow for efficient parallelization of computationally intensive tasks. Service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity. Used to find haplotype segments and reference panel of sequenced genomes, assign genotypes at untyped markers, improve genome coverage, facilitate comparison and combination of studies that use different marker panels, increase power to detect genetic association, and guide fine mapping.

Proper citation: Michigan Imputation Server (RRID:SCR_017579) Copy   

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http://pepr.cnmcresearch.org/

An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ).

Proper citation: Public Expression Profiling Resource (RRID:SCR_007274) Copy   

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http://idash.ucsd.edu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. National Center for Biomedical Computing (NCBC) that develops new algorithms, opensource tools, computational infrastructure, and services for biomedical and behavioral researchers nationwide to promote the secure sharing and consuming of biomedical and behavioral resources (software, data, and computing systems) with iDASH collaborators. The center addresses fundamental challenges to research progress by providing a secure, privacypreserving environment in which researchers can analyze genomic, transcriptomic, clinical, behavioral, and social data relevant to health. Three driving biological projects in iDASH (Molecular Phenotyping of Kawasaki Disease, Post-Marketing Surveillance of Hematologic Medications, and Individualized Intervention to Enhance Physical Activity) span the molecular-individualpopulation spectrum, and they will motivate, inform, and support tool development. iDASH will collaborate with other NCBCs and will disseminate tools via annual workshops, presentations at major conferences, and scientific publications.

Proper citation: iDASH (RRID:SCR_003524) Copy   

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http://www.bumc.bu.edu/cardiovascularproteomics/cpctools/strap/

Software program that automatically annotates a protein list with information that helps in the meaningful interpretation of data from mass spectrometry and other techniques. It takes protein lists as input, in the form of plain text files, protXML files (usually from the TPP), or Dat files from MASCOT search results. From this, it generates protein annotation tables, and a variety of GO charts to aid individual and differential analysis of proteomics data. It downloads information from mainly the Uniprot and EBI QuickGO databases. STRAP requires Windows XP or higher with at least version 3.5 of the Microsoft .NET Framework installed. Platform: Windows compatible

Proper citation: STRAP (RRID:SCR_005675) Copy   

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http://www.mouse-genome.bcm.tmc.edu/ENU/MutagenesisProj.asp

THIS RESOURCE IS NO LONGER IN SERVICE. For updated mutant information, please visit MMRRC or The Jackson Laboratory. Produces, characterizes, and distributes mutant mouse strains with defects in embryonic and postembryonic development. The goal of the ENU Mutagenesis project III is to determine the function of genes on mouse Chromosome 11 by saturating the chromosome with recessive mutations. The distal 40 cM of mouse Chr 11 exhibits linkage conservation with human Chromosome 17. We are using the chemical N-ethyl-N-nitrosourea (ENU) to saturate wild type chromosomes with point mutations. By determining the function of genes on a mouse chromosome, we can extrapolate to predict function on a human chromosome. We expect many of the new mutants to represent models of human diseases such as birth defects, patterning defects, growth and endocrine defects, neurological anomalies, and blood defects. Because many of the mutations we expect to isolate may be lethal or detrimental to the mice, we are using a unique approach to isolate mutations. This approach uses a balancer chromosome that is homozygous lethal and carries a dominant coat color marker to suppress recombination over a reasonable interval.

Proper citation: Mouse Mutagenesis Center for Developmental Defects (RRID:SCR_007321) Copy   

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https://rgd.mcw.edu/QueryBuilder/

Software text mining tool aiding curation at Rat Genome Database. Ontology driven, concept based literature search engine developed at RGD. Tags abstracts with gene names, gene mutations, organism names and terms from ontologies vocabularies used at RGD. Open and fully customizable.

Proper citation: OntoMate (RRID:SCR_018493) Copy   

•   Source: SciCrunch Registry

http://www.census.gov/did/www/nlms/

A database based on a random sample of the noninstitutionalized population of the United States, developed for the purpose of studying the effects of demographic and socio-economic characteristics on differentials in mortality rates. It consists of data from 26 U.S. Current Population Surveys (CPS) cohorts, annual Social and Economic Supplements, and the 1980 Census cohort, combined with death certificate information to identify mortality status and cause of death covering the time interval, 1979 to 1998. The Current Population Surveys are March Supplements selected from the time period from March 1973 to March 1998. The NLMS routinely links geographical and demographic information from Census Bureau surveys and censuses to the NLMS database, and other available sources upon request. The Census Bureau and CMS have approved the linkage protocol and data acquisition is currently underway. The plan for the NLMS is to link information on mortality to the NLMS every two years from 1998 through 2006 with research on the resulting database to continue, at least, through 2009. The NLMS will continue to incorporate data from the yearly Annual Social and Economic Supplement into the study as the data become available. Based on the expected size of the Annual Social and Economic Supplements to be conducted, the expected number of deaths to be added to the NLMS through the updating process will increase the mortality content of the study to nearly 500,000 cases out of a total number of approximately 3.3 million records. This effort would also include expanding the NLMS population base by incorporating new March Supplement Current Population Survey data into the study as they become available. Linkages to the SEER and CMS datasets are also available. Data Availability: Due to the confidential nature of the data used in the NLMS, the public use dataset consists of a reduced number of CPS cohorts with a fixed follow-up period of five years. NIA does not make the data available directly. Research access to the entire NLMS database can be obtained through the NIA program contact listed. Interested investigators should email the NIA contact and send in a one page prospectus of the proposed project. NIA will approve projects based on their relevance to NIA/BSR''s areas of emphasis. Approved projects are then assigned to NLMS statisticians at the Census Bureau who work directly with the researcher to interface with the database. A modified version of the public use data files is available also through the Census restricted Data Centers. However, since the database is quite complex, many investigators have found that the most efficient way to access it is through the Census programmers. * Dates of Study: 1973-2009 * Study Features: Longitudinal * Sample Size: ~3.3 Million Link: *ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00134

Proper citation: National Longitudinal Mortality Study (RRID:SCR_008946) Copy   

•   Source: SciCrunch Registry

https://biolincc.nhlbi.nih.gov/home/

Repository that serves to coordinate searches across data and biospecimen collections from participants in numerous clinical trials and epidemiologic studies and to provide an electronic means for requests for additional information and the submission of requests for collections. The collections, comprising data from more than 80 trials or studies and millions of biospecimens, are available to qualified investigators under specific terms and conditions consistent with the informed consents provided by the individual study participants. Some datasets are presented with studies and supporting materials to facilitate their use in reuse and teaching. Datasets support basic research, clinical studies, observational studies, and demonstrations. Researchers wishing to apply to submit biospecimen collections to the NHLBI Biorepository for sharing with qualified investigators may also use this website to initiate that process.

Proper citation: Biologic Specimen and Data Repository Information Coordinating Center (BioLINCC) (RRID:SCR_013142) Copy   

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http://hb.flatironinstitute.org/

Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations.

Proper citation: HumanBase (RRID:SCR_016145) Copy   

•   Source: SciCrunch Registry

https://signalingpathways.org

Web multi omics knowledgebase based upon public, manually curated transcriptomic and cistromic datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Integrated omics knowledgebase for mammalian cellular signaling pathways. Web browser interface was designed to accommodate numerous routine data mining strategies. Datasets are biocurated versions of publically archived datasets and are formatted according to recommendations of the FORCE11 Joint Declaration on Data Citation Principles73, and are made available under Creative Commons CC 3.0 BY license. Original datasets are available.

Proper citation: Signaling Pathways Project (RRID:SCR_018412) Copy   

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https://reprint-apms.org/?q=chooseworkflow

Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions.

Proper citation: CRAPome (RRID:SCR_025008) Copy   

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https://github.com/calico/borzoi

Software package to access the Borzoi models, which are convolutional neural networks trained to predict RNA-seq coverage at 32bp resolution given 524kb input sequences.

Proper citation: Borzoi (RRID:SCR_026619) Copy   

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https://github.com/QuackenbushLab/NetworkDataCompanion

Software R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo. Streamlines routine steps in TCGA data processing, including filtering and mapping gene and sample identifiers between modalities and allows modality-specific data transformation, such as normalization and cleaning.

Proper citation: NetworkDataCompanion (RRID:SCR_026532) Copy   

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https://predictomes.org/

Interactive database of protein protein interactions modeled by AlphaFold multimer. Classifier-curated database of AlphaFold-modeled protein-protein interactions.

Proper citation: Predictomes (RRID:SCR_026691) Copy   

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https://github.com/williamslab/ped-sim

Software tool to simulate pedigree structures. Used for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either model of crossover interference or traditional Poisson model for inter-crossover distances.

Proper citation: ped-sim (RRID:SCR_026957) Copy   

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https://github.com/itmat/BEERS2

Software for simulation of RNA-seq reads. Combines flexible and highly configurable design with detailed simulation of entire library preparation and sequencing pipeline and is designed to include effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification.

Proper citation: BEERS2 (RRID:SCR_027287) Copy   

•   Source: SciCrunch Registry