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https://generanger.maayanlab.cloud/gene/A2M?database=ARCHS4

Web server application that provides access to processed data about expression of human genes and proteins across human cell types, tissues, and cell lines from several atlases. Used to explore single gene expression across tissues and cell types.

Proper citation: GeneRanger (RRID:SCR_023622) Copy   

•   Source: SciCrunch Registry

https://targetranger.maayanlab.cloud/

Web server application that identifies targets from user inputted RNA-seq samples collected from cells we wish to target. By comparing inputted samples with processed RNA-seq and proteomics data from several atlases, TargetRanger identifies genes that are highly expressed in target cells while lowly expressed across normal human cell types, tissues, and cell lines.

Proper citation: TargetRanger (RRID:SCR_023621) Copy   

•   Source: SciCrunch Registry

http://www.hemonc.org

Medical wiki of interventions, regimens, and general information relevant to fields of hematology and oncology. Knowledge base for hematology and oncology providers, containing details about hematology/oncology drugs and treatment regimens. Any healthcare professional can sign up to contribute. Acuracy and completeness of content is overseen by Editorial Board.

Proper citation: HemOnc Knowledgebase (RRID:SCR_023436) Copy   

•   Source: SciCrunch Registry

https://seer.cancer.gov/siterecode/icdo3_dwhoheme/index.html

Website describing International Classification of Diseases-Oncology codes that corresponds to different cancer sites in the Surveillance, Epidemiology, and End Results (SEER) registry.

Proper citation: NCI Site Recode ICD-O-3/WHO 2008 Definition (RRID:SCR_024687) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://rulai.cshl.edu/tred

Collects mammalian cis- and trans-regulatory elements together with experimental evidence. Regulatory elements were mapped on to assembled genomes. Resource for gene regulation and function studies. Users can retrieve primers, search TF target genes, retrieve TF motifs, search Gene Regulatory Networks and orthologs, and make use of sequence analysis tools. Uses databases such as Genbank, EPD and DBTSS, and employ promoter finding program FirstEF combined with mRNA/EST information and cross-species comparisons. Manually curated.

Proper citation: Transcriptional Regulatory Element Database (RRID:SCR_005661) Copy   

•   Source: SciCrunch Registry

https://www.jax.org/jax-mice-and-services/in-vivo-pharmacology/mouse-tumor-biology-database

Database supports use of mouse model system for human cancer by providing comprehensive resource for data and information on various tumor models.

Proper citation: Mouse Tumor Biology Database (RRID:SCR_006517) Copy   

•   Source: SciCrunch Registry

http://epi.grants.cancer.gov/CFR/

The Breast Cancer Family Registry (Breast CFR) and the Colon Cancer Family Registry (Colon CFR) were established by the National Cancer Institute (NCI) as a unique resource for investigators to use in conducting studies on the genetics and molecular epidemiology of breast and colon cancer. Known collectively as the CFRs, they share a central goal: the translation of research to the clinical and prevention settings for the benefit of Registry participants and the general public. The CFRs are particularly interested in: * Identifying and characterizing cancer susceptibility genes; * Defining gene-gene and gene-environment interactions in cancer etiology; and * Exploring the translational, preventive, and behavioral implications of research findings. The CFRs do not provide funding for studies; however, researchers can apply to access CFR data and biospecimens contributed by thousands of families from across the spectrum of risk for these cancers and from population-based or relative controls. Special features of the CFRs include: * Population-based and clinic-based ascertainment; * Systematic collection of validated family history; * Epidemiologic risk factor , clinical, and followup data; * Biospecimens (including tumor blocks and Epstein-Barr virus (EBV)-transformed cell lines); * Ongoing molecular characterization of the participating families; and * A combined informatics center.

Proper citation: NCI Breast and Colon Cancer Family Registries (RRID:SCR_006664) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://taylor0.biology.ucla.edu/structureHarvester/

Web based program for collating results generated by program STRUCTURE. Provides assess and visualize likelihood values across multiple values of K and hundreds of iterations for easier detection of number of genetic groups that best fit data. Reformats data for use in downstream programs, such as CLUMPP.It is complement for using software Structure in genetics population. Website and program for visualizing STRUCTURE output and implementing Evanno method., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Structure Harvester (RRID:SCR_017636) Copy   

•   Source: SciCrunch Registry

http://statistika.mfub.bg.ac.rs/interactive-linegraph/

Interactive web based tool for creating line graphs for scientific publications. Users can view different summary statistics, examine lines for any individual in data, focus on time points or groups of interest, and view changes between any two time points and conditions.

Proper citation: Interactive Line Graph (RRID:SCR_018334) Copy   

•   Source: SciCrunch Registry

https://cadd.gs.washington.edu/

Web tool for predicting deleteriousness of variants throughout human genome. Software tool for scoring deleteriousness of single nucleotide variants as well as insertion and deletions variants in human genome.

Proper citation: Combined Annotation Dependent Depletion (RRID:SCR_018393) Copy   

•   Source: SciCrunch Registry

http://www.cpc.unc.edu/projects/addhealth

Longitudinal study of a nationally representative sample of adolescents in grades 7-12 in the United States during the 1994-95 school year. Public data on about 21,000 people first surveyed in 1994 are available on the first phases of the study, as well as study design specifications. It also includes some parent and biomarker data. The Add Health cohort has been followed into young adulthood with four in-home interviews, the most recent in 2008, when the sample was aged 24-32. Add Health combines longitudinal survey data on respondents social, economic, psychological and physical well-being with contextual data on the family, neighborhood, community, school, friendships, peer groups, and romantic relationships, providing unique opportunities to study how social environments and behaviors in adolescence are linked to health and achievement outcomes in young adulthood. The fourth wave of interviews expanded the collection of biological data in Add Health to understand the social, behavioral, and biological linkages in health trajectories as the Add Health cohort ages through adulthood. The restricted-use contract includes four hours of free consultation with appropriate staff; after that, there''s a fee for help. Researchers can also share information through a listserv devoted to the database.

Proper citation: Add Health (National Longitudinal Study of Adolescent Health) (RRID:SCR_007434) Copy   

•   Source: SciCrunch Registry

http://rulai.cshl.edu/cgi-bin/tools/ESE3/esefinder.cgi?process=home

A web-based resource that facilitates rapid analysis of exon sequences to identify putative exonic splicing enhancers (ESEs) responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements.

Proper citation: ESEfinder 3.0 (RRID:SCR_007088) Copy   

•   Source: SciCrunch Registry

http://www.oreganno.org/oregano/

Open source, open access database and literature curation system for community based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. Automatically cross referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, eVOC: Cell type ontology, and Taxonomy database. Community driven resource for curated regulatory annotation.

Proper citation: Open Regulatory Annotation Database (RRID:SCR_007835) Copy   

•   Source: SciCrunch Registry

http://cabig.cancer.gov

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 19, 2016. It has been integrated into the National Cancer Informatics Program (NCIP). The National Cancer Institute launched the cancer Biomedical Informatics Grid (caBIG) to create a virtual network of interconnected data, individuals, and organizations that worked together to redefine how cancer research is conducted. caBIG capabilities allowed researchers and clinicians to collaborate more effectively so that complex research questions might be asked and answered faster and more effectively. The mission of caBIG was to develop a truly collaborative information network that accelerated the discovery of new approaches for the detection, diagnosis, treatment, and prevention of cancer, ultimately improving patient outcomes.

Proper citation: Cancer Biomedical Informatics Grid (RRID:SCR_003328) Copy   

•   Source: SciCrunch Registry

http://www.cbioportal.org/

A portal that provides visualization, analysis and download of large-scale cancer genomics data sets.

Proper citation: cBioPortal (RRID:SCR_014555) Copy   

•   Source: SciCrunch Registry

https://genome.ucsc.edu/cgi-bin/hgLiftOver

Web tool to convert genome coordinates and genome annotation files between assemblies. Used to translate genomic coordinates from one assembly version into another and retrieves putative orthologous regions in other species using UCSC chained and netted alignments.

Proper citation: liftOver (RRID:SCR_018160) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/mosdepth

Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes.

Proper citation: mosdepth (RRID:SCR_018929) Copy   

•   Source: SciCrunch Registry

http://www.med.upenn.edu/genetics/dnaseq/index.shtml

Core facility that provides the following services: Large sequencing project support, Sanger sequencing service, High throughput DNA sequencing, Ion Torrent Personal Genome Machine sequencing, Template preparation and purification, Roche 454 sequencing, Sequence analysis and database search support, Construction of targeting vector for gene targeting, Genotyping and Fragment Analysis service, Molecular biology services, Mouse genotyping, and Ion Personal Genome Machine sequencing data analysis. The DNA Sequencing Facility provides long read, automated Sanger sequencing; microsatellite-based genotyping and fragment analysis; plasmid and BAC DNA preparation and purification; and related molecular biological services including PCR, cloning, sub-cloning, site-directed mutagenesis, and preparation of targeting vectors for gene targeting in mice. Core also provides services and support for analysis and interpretation of sequence data as well as the design of approaches to complex sequencing projects. For the last four years the facility has been providing Roche 454 sequencing service that includes library preparation, emulsion PCR and pyrosequencing for both genomic DNA and amplicons.

Proper citation: University of Pennsylvania Genomics Analysis Core (RRID:SCR_011061) Copy   

•   Source: SciCrunch Registry