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https://www.sbpdiscovery.org/

Conducts world class collaborative research dedicated to finding cures for human disease, improving quality of life, and thus creating a legacy for its employees, partners, donors, and community. SBP is dedicated to discovering the fundamental molecular causes of disease and devising the innovative therapies of tomorrow. Has established major research programs in cancer, neurodegeneration, diabetes, and infectious, inflammatory, and childhood diseases. SBP is a U.S.-based, non-profit public benefit corporation, with operations in San Diego (La Jolla) and Orlando (Lake Nona) in Florida.

Proper citation: Sanford Burnham Prebys Medical Discovery Institute (RRID:SCR_011516) Copy   

•   Source: SciCrunch Registry

http://www.moffitt.org/

H. Lee Moffitt Cancer Center & Research Institute has made a lasting commitment to the prevention and cure of cancer, working tirelessly in the areas of patient care, research and education to advance one step further in fighting this disease. As part of an elite group of National Cancer Institute (NCI) Comprehensive Cancer Centers, Moffitt focuses on the development of early stage translational research aimed at the rapid translation of scientific discoveries to benefit patient care. Since the first patient admission in October 1986, Moffitt physicians, scientists and staff members have worked together to establish a tradition of excellence offered in an atmosphere characterized by kindness, caring and hope. The Cancer Center''s future growth in clinical care and research rests firmly on this tradition and makes possible the changes ahead. The mission of Moffitt Cancer Center is to contribute to the prevention and cure of cancer. Moffitt''s vision is to be the leader in scientific discovery and translation into compassionate care, cures, and prevention of cancer for our community and the world. As it grows to fulfill its mission, the Cancer Center will continue to be distinguished by its compassionate and effective patient care. Moffitt Cancer Center is a not-for-profit institution. It includes private patient rooms, the Southeast''s largest Blood and Marrow Transplant Program, outpatient treatment programs that record more than 320,500 visits a year, the Moffitt Research Center, Moffitt Cancer Center at International Plaza and the Lifetime Cancer Screening & Prevention Center.

Proper citation: Moffitt Cancer Center (RRID:SCR_008730) Copy   

•   Source: SciCrunch Registry

http://www.cbtrus.org/

Voluntary, non-profit organization dedicated to collecting and disseminating statistical data. Resource for gathering and disseminating epidemiologic data on all primary benign and malignant brain and other CNS tumors.

Proper citation: Central Brain Tumor Registry of the United States (RRID:SCR_008748) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301786/

Device to control spatial and temporal variations in oxygen tensions to better replicate in vivo biology. Consists of three parallel connected tissue chambers and oxygen scavenger channel placed adjacent to these tissue chambers. Provides consistent control of spatial and temporal oxygen gradients in tissue microenvironment and can be used to investigate important oxygen dependent biological processes present in cancer, ischemic heart disease, and wound healing.

Proper citation: Microfluidic device to attain high spatial and temporal control of oxygen (RRID:SCR_017131) Copy   

•   Source: SciCrunch Registry

http://www.dana-farber.org/

Cancer institute that provides expert, compassionate care to children and adults with cancer while advancing the understanding, diagnosis, treatment, cure, and prevention of cancer and related diseases. As an affiliate of Harvard Medical School and a Comprehensive Cancer Center designated by the National Cancer Institute, the Institute also provides training for new generations of physicians and scientists, designs programs that promote public health particularly among high-risk and underserved populations, and disseminates innovative patient therapies and scientific discoveries to their target community across the United States and throughout the world.

Proper citation: Dana-Farber Cancer Institute (RRID:SCR_003040) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/proteomecommons-tranche/

A distributed file storage system that you can upload files to and download files from. All files uploaded to the repository are replicated several times to protect against their accidental loss. Files uploaded to the repository can be of any size, can be of any file type, and can be encrypted with a passphrase of your choosing. The Proteome Commons Tranche repository is the first instance of a Tranche repository. Tranche, was created so that anybody can take it and make their own Tranche repository. This is the first implementation of the Tranche software, and is useful as a test bed for the software. This repository relies on educational institutions to provide the hardware and facilities for Tranche servers. While we maintain a set of servers, the continued growth of this public resource will rely on the generosity of the institutions that use the repository most.

Proper citation: Proteome Commons Tranche repository (RRID:SCR_003441) Copy   

•   Source: SciCrunch Registry

https://github.com/genome/bam-readcount

Software tool that runs on BAM or CRAM file and generates low level information about sequencing data at specific nucleotide positions. Its outputs include observed bases, readcounts, summarized mapping and base qualities, strandedness information, mismatch counts, and position within the reads.

Proper citation: bam readcount (RRID:SCR_023653) Copy   

•   Source: SciCrunch Registry

http://www.pathology.med.ohio-state.edu/HTRN/apc/default.asp

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The Adenoma Polyp Tissue Bank (APTB) receives whole blood from patients enrolled in the Prevention of Sporadic Colorectal Adenomas with Celecoxib clinical trial. We have reached our accrual on blood submissions, so we will no longer be receiving blood specimens The objectives of this trial are as follows: A. To determine the efficacy and safety of celecoxib versus placebo in preventing the occurrence of newly detected colorectal adenomas in subjects at increased risk for colorectal carcinoma. In addition to incidence, other established risk factors will be evaluated for their association with occurrence of new colorectal adenomas, including cancer family history and adenoma size, histopathologic grade, multiplicity and location. Primary assessment of treatment efficacy will be the reduction in the number of subjects with adenomas at colonoscopy after Year 1 and Year 3 of study drug use. Secondary assessments of treatment efficacy will be 1) the number of adenomas 2) the histopathologic grade of adenomas and 3) the size of adenomas, also measured after one year and three years of study drug use. These factors will be incorporated into a risk model for predicting adenoma occurrence and response to celecoxib. B. To determine the efficacy of celecoxib versus placebo in modulating one or more of a panel of biomarkers for colorectal cancer at the cellular and molecular level sampled in a subset of subjects at selective sites at baseline and after Year 1 and Year 3 of study drug use. These biomarkers will include measurements of aberrant crypt foci (ACF), proliferation (index and crypt distribution), apoptosis (index and crypt distribution), COX expression and activity. If modulation of one or more mucosal biomarkers occur, we will explore whether it correlates with the development of incident colorectal neoplasia (adenomas/carcinomas), thereby attempting to validate the surrogacy of that biomarker. C. To develop a specimen bank. Serum and white blood cells are isolated from whole blood and adenoma tissue blocks and slides are banked. Banked specimens will become available for use in correlative science studies at a later point. This project began in 1999 and will be extended through 2006. The lead principal investigator is Monica M. Bertagnolli, MD, Brigham and Women''s Hospital, Boston, MA, and the APTB Director is Scott Jewell, Ph.D., Department of Pathology, The Ohio State University. The APTB is supported by the NIH, NCI Division of Cancer Prevention, in connection with the Strang Cancer Prevention Center, Cornell University, New York., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Adenoma Polyp Tissue Bank (RRID:SCR_005366) Copy   

•   Source: SciCrunch Registry

https://github.com/mskilab-org/JaBbA

Software tool to infer junction-balanced genome graphs with high fidelity. Builds genome graph based on junctions and read depth from whole genome sequencing, inferring optimal copy numbers for both vertices (DNA segments) and edges (bonds between segments).

Proper citation: JaBba (RRID:SCR_027134) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/sivic/

Software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies.

Proper citation: Spectroscopic Imaging, VIsualization, and Computing (SIVIC) (RRID:SCR_027875) Copy   

•   Source: SciCrunch Registry

https://pancreatlas.org/

Collection of human pancreas data and images. Platform to share data from human pancreas samples. Houses reference datasets from human pancreas samples, achieved through generosity of organ donors and their families.

Proper citation: Pancreatlas (RRID:SCR_018567) Copy   

•   Source: SciCrunch Registry

https://www.robotreviewer.net/

Software tool as machine learning system that automatically assesses bias in clinical trials. From PDF formatted trial report determines risks of bias for domains defined by Cochrane Risk of Bias (RoB) tool, and extracts supporting text for these judgments.

Proper citation: Robot Reviewer (RRID:SCR_018961) Copy   

•   Source: SciCrunch Registry

http://www.karmanos.org/

Center for patient care, education and research on cancer. The institute focuses its research on prevention methods, early detection, treatment and finding cures.

Proper citation: Karmanos Cancer Institute (RRID:SCR_000508) Copy   

•   Source: SciCrunch Registry

http://discover.nci.nih.gov/gominer/

GoMiner is a tool for biological interpretation of "omic" data including data from gene expression microarrays. Omic experiments often generate lists of dozens or hundreds of genes that differ in expression between samples, raising the question, What does it all mean biologically? To answer this question, GoMiner leverages the Gene Ontology (GO) to identify the biological processes, functions and components represented in these lists. Instead of analyzing microarray results with a gene-by-gene approach, GoMiner classifies the genes into biologically coherent categories and assesses these categories. The insights gained through GoMiner can generate hypotheses to guide additional research. GoMiner displays the genes within the framework of the Gene Ontology hierarchy in two ways: * In the form of a tree, similar to that in AmiGO * In the form of a "Directed Acyclic Graph" (DAG) The program also provides: * Quantitative and statistical analysis * Seamless integration with important public databases GoMiner uses the databases provided by the GO Consortium. These databases combine information from a number of different consortium participants, include information from many different organisms and data sources, and are referenced using a variety of different gene product identification approaches.

Proper citation: GoMiner (RRID:SCR_002360) Copy   

•   Source: SciCrunch Registry

https://github.com/humanlongevity/HLA

Software tool for fast and accurate HLA typing from short read sequence data. Iteratively refines mapping results at amino acid level to achieve four digit typing accuracy for both class I and II HLA genes, taking only 3 min to process 30× whole genome BAM file on desktop computer.

Proper citation: xHLA (RRID:SCR_022277) Copy   

•   Source: SciCrunch Registry

https://github.com/RabadanLab/arcasHLA

Software tool for high resolution HLA typing from RNAseq. Fast and accurate in silico inference of HLA genotypes from RNA-seq.

Proper citation: arcasHLA (RRID:SCR_022286) Copy   

•   Source: SciCrunch Registry

https://cytotrace.stanford.edu/

Software tool that predicts differentiation state of cells from single cell RNA sequencing data. Used for predicting differentiation states from scRNA-seq data.

Proper citation: CytoTRACE (RRID:SCR_022828) Copy   

•   Source: SciCrunch Registry

https://appyters.maayanlab.cloud

Collection of web-based software applications that enable users to execute bioinformatics workflows without coding. Turns Jupyter notebooks into fully functional standalone web-based bioinformatics applications. Each Appyter application introduces data entry form for uploading or fetching data, as well as for selecting options for various settings. Once user presses Submit, Appyter is executed in cloud and user is presented with Jupyter Notebook report that contain results. Report includes markdown text, interactive and static figures, and source code. Appyter users can share the link to the output report, as well as download the fully executable notebook for execution on other platforms.

Proper citation: Appyters (RRID:SCR_021245) Copy   

•   Source: SciCrunch Registry

http://crispor.tefor.net

Web application that helps design, evaluate and clone guide sequences for the CRISPR/Cas9 system. This sgRNA design tool assists with guide selection in a variety of genomes and pre-calculated results for all human coding exons as a UCSC Genome Browser track.

Proper citation: CRISPOR (RRID:SCR_015935) Copy   

•   Source: SciCrunch Registry

http://discover.nci.nih.gov/gominer/GoCommandWebInterface.jsp

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A web program that organizes lists of genes of interest (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology and automates the analysis of multiple microarrays then integrates the results across all of them in exportable output files and visualizations. High-Throughput GoMiner is an enhancement of GoMiner and is implemented with both a command line interface and a web interface. The program can also: efficiently perform automated batch processing of an arbitrary number of microarrays; produce a human- or computer-readable report that rank-orders the multiple microarray results according to the number of significant GO categories; integrate the multiple microarray results by providing organized, global clustered image map visualizations of the relationships of significant GO categories; provide a fast form of false discovery rate multiple comparisons calculation; and provide annotations and visualizations for relating transcription factor binding sites to genes and GO categories.

Proper citation: High-Throughput GoMiner (RRID:SCR_000173) Copy   

•   Source: SciCrunch Registry