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http://www.stanford.edu/group/exonarray/cgi-bin/plot_selector.pl

Transcriptome database of acutely isolated purified astrocytes, neurons, and oligodendrocytes. Provides improved cell-type-specific markers for better understanding of neural development, function, and disease.

Proper citation: Exon Array Browser (RRID:SCR_008712) 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

https://github.com/hetio/hetmatpy

Software Python package for matrix storage and operations on hetnets. Enables identifying relevant network connections between set of query nodes.

Proper citation: HetMatPy (RRID:SCR_023409) Copy   

•   Source: SciCrunch Registry

https://maayanlab.cloud/X2K

Web service to predict involvement of upstream cell signaling pathways, given signature of differentially expressed genes. Used to linking expression signatures to upstream cell signaling networks.

Proper citation: X2K Web (RRID:SCR_023624) Copy   

•   Source: SciCrunch Registry

https://www.cancermodels.org/

Cancer research platform that aggregates clinical, genomic and functional data from various types of patient derived cancer models, xenographs, organoids and cell lines. Open catalog of harmonised patient-derived cancer models. Standardises, harmonises and integrates clinical metadata, molecular and treatment-based data from academic and commercial providers worldwide. Data is FAIR and underpins generation and testing of new hypotheses in cancer mechanisms and personalised medicine development. PDCM Finder have expanded to organoids and cell lines and is now called CancerModels.Org. PDCM Finder was launched in April 2022 as successor of PDX Finder portal, which focused solely on patient-derived xenograft models.

Proper citation: CancerModels.Org (RRID:SCR_023931) Copy   

•   Source: SciCrunch Registry

http://rnainformatics.org.cn/RiboToolkit/

Integrated web server developed for Ribo-seq data analysis. Platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution.Web based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs.

Proper citation: RiboToolkit (RRID:SCR_024406) Copy   

•   Source: SciCrunch Registry

https://www.robotreviewer.net/about

Open source web based system that uses machine learning and NLP to semi automate biomedical evidence synthesis, to aid practice of Evidence Based Medicine. Processes full text journal articles describing randomized controlled trials. Designed to automatically extract key data items from reports of clinical trials.

Proper citation: RobotReviewer (RRID:SCR_021064) Copy   

•   Source: SciCrunch Registry

https://github.com/r3fang/SnapATAC

Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset.

Proper citation: SnapATAC (RRID:SCR_020981) Copy   

•   Source: SciCrunch Registry

https://www.synapse.org/#!Synapse:syn22345748/wiki/605339

Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets.

Proper citation: Exemplar Microscopy Images of Tissues (RRID:SCR_021052) 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

https://github.com/abyzovlab/CNVpytor

Software Python package and command line tool for CNV/CNA analysis from depth of coverage by mapped reads. Software tool for CNV/CNA detection and analysis from read depth and allele imbalance in whole genome sequencing.

Proper citation: CNVpytor (RRID:SCR_021627) Copy   

•   Source: SciCrunch Registry

https://cumulus.readthedocs.io/en/stable

Software tool as cloud based single cell genomics and spatial transcriptomics data analysis framework that is scalable to massive amounts of data and able to process variety of data types. Consists of cloud analysis workflow, Python analysis package and visualization application. Supports analysis of single-cell RNA-seq, CITE-seq, Perturb-seq, single-cell ATAC-seq, single-cell immune repertoire and spatial transcriptomics data.

Proper citation: Cumulus (RRID:SCR_021644) Copy   

•   Source: SciCrunch Registry

http://www.bionet.umn.edu/tpf/home.html

Procure and distribute human tissue and other biological samples in support of basic, translational, and clinical cancer research at the University of Minnesota. The TPF is a centralized resource with standardized patient consent, sample collection, processing, storage, quality control, distribution, and electronic record maintenance. Since the 1996 inception of the TPF, over 61,000 tissue samples including well-preserved samples of malignant and benign tumors, organ-matched normal tissue, and other types of diseased tissues, have been collected from surgical specimens obtained at the University of Minnesota Medical Center-Fairview (UMMC-F) University Campus. Surgical pathologists are intellectually engaged in TPF functions, providing researchers with specimen-oriented medical consultation to facilitate research productivity. Prior to surgery, TPF personnel identify and consent patients for procurement of tissue, blood, urine, saliva, and ascites fluid. Within the integrated working environment of the surgical pathology laboratory, freshly obtained tissues not needed for diagnosis are selected and provided by pathologists to TPF personnel. Tissue samples are then assigned an independent code and processed. TPF staff can also work with researchers to individualize the procurement of tissues to fit specific research needs.

Proper citation: University of Minnesota Tissue Procurement Facility (RRID:SCR_004270) Copy   

•   Source: SciCrunch Registry

http://acsr.ucsf.edu/

A biorepository for HIV-infected human biospecimens from a wide spectrum of HIV-related or associated diseases, including cancer, and from appropriate HIV-negative controls. The ACSR has formalin-fixed paraffin embedded biospecimens, fresh frozen biospecimens, malignant cell suspensions, fine needle aspirates, and cell lines from patients with HIV-related malignancies. It also contains serum, plasma, urine, bone marrow, cervical and anal specimens, saliva, semen, and multi-site autopsy speicmens from patients with HIV-related malignancies including those who have participated in clinical trials. The ACSR has an associated databank that contains prognostic, staging, outcome and treatment data on patients from whom tissues were obtained. The ACSR database contains more than 300,000 individual biospecimens with associated clinical information. Biospecimens are entered into the ACSR database by processing type, disease category, and number of cases defined by disease category.

Proper citation: AIDS and Cancer Specimen Resource (RRID:SCR_004216) Copy   

•   Source: SciCrunch Registry

http://www.nsabp.pitt.edu/NSABP_Pathology.asp

The NSABP (National Surgical Adjuvant Breast and Bowel Project) Tissue Bank is the central repository of tissue samples (stained and unstained slides, tissue blocks, and frozen tissue specimens) collected from clinical trials conducted by the NSABP. The main scientific aim of the NSABP Division of Pathology is to develop clinical context-specific prognostic markers and predictive markers that predict response to or benefit from specific therapeutic modality. To achieve this aim, the laboratory collects the tumor and adjacent normal tissues from cancer patients enrolled into the NSABP trials through its membership institutions, and maintain these valuable materials with clinical follow-up information and distribute them to qualified approved investigators. Currently, specimens from more than 90,000 cases of breast and colon cancer are stored and maintained at the bank. Paraffin embedded tumor specimens are available from NSABP trials. We currently do not bank frozen tissues. All blocks are from patients enrolled in prospective NSABP treatment protocols and complete clinical follow up information as well as demographic information is available. Depending on the project, unstained tissue sections of 4-micrometer thickness, tissue microarrays, or stained slides are provided to the investigators in a blinded study format. Any investigators with novel projects that conform to the research goals of NSABP may apply for the tissue. Please refer to the NSABP Tissue Bank Policy to determine if your project conforms to these goals. Priority is given to NSABP membership institutions who regularly submit tissue blocks.

Proper citation: National Surgical Adjuvant Breast and Bowel Project Tissue Bank (RRID:SCR_004506) Copy   

•   Source: SciCrunch Registry

http://pluto3.nci.nih.gov/tissue/default.cfm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Specimen Resource Locator is a database to help researchers locate human specimens (tissue, serum, DNA/RNA, other specimens) for cancer research. It includes tissue banks and tissue procurement systems with access to normal, benign, precancerous and cancerous human tissue from a variety of organs. Researchers specify the types of specimens, number of cases, preservation methods and associated data they require. The Locator will then search the database and return a list of tissue resources most likely to meet their requirements. When no match is obtained, the researcher is referred to the NCI Tissue Expediter ([email protected]). The Tissue expediter is a scientist who can help researchers identify appropriate resources and/or appropriate collaborators.

Proper citation: NCI Specimen Resource Locator (RRID:SCR_004754) Copy   

•   Source: SciCrunch Registry

https://seer.cancer.gov/csr/1975_2016/

Platform to report outlining trends in cancer statistics and methods to derive various cancer statistics from the Surveillance, Epidemiology, and End Results (SEER) program. Authoritative source for cancer statistics in the United States.

Proper citation: NCI SEER Cancer Statistics Review (RRID:SCR_024685) Copy   

•   Source: SciCrunch Registry

https://seer.cancer.gov/lymphomarecode/lymphoma-2020.html

Website describing International Classification of Diseases codes that corresponds to lymphomas in the Surveillance, Epidemiology, and End Results (SEER) registry.

Proper citation: NCI Lymphoid Neoplasm Recode 2020 Revision Definition (RRID:SCR_024686) 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

https://openmm.org/

Software toolkit to run modern molecular simulations. It can be used either as a standalone application for running simulations, or as a library that enables accelerated calculations for molecular dynamics on high-performance computer architectures.

Proper citation: OpenMM (RRID:SCR_000436) Copy   

•   Source: SciCrunch Registry