Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://www.bioconductor.org/packages/release/bioc/html/sesame.html
Software R package for reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions.
Proper citation: SeSAMe (RRID:SCR_027388) Copy
https://weghornlab.org/software.html
Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer.
Proper citation: CBaSE (RRID:SCR_027765) Copy
https://github.com/McGranahanLab/TcellExTRECT
Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes.
Proper citation: T Cell ExTRECT (RRID:SCR_027742) Copy
https://github.com/vanallenlab/comut
Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots.
Proper citation: CoMUT (RRID:SCR_027745) Copy
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
https://bioconductor.org/packages/release/bioc/html/tximeta.html
Software R package for reference sequence checksums for provenance identification in RNA-seq. Performs numerous annotation and metadata gathering tasks on behalf of users during the import of transcript counts and abundance from quantification tools such as salmon. Data are imported as SummarizedExperiment objects with associated GenomicRanges metadata. Correct metadata is added automatically via reference sequence digests, facilitating genomic analyses and assisting in computational reproducibility.
Proper citation: tximeta (RRID:SCR_028005) Copy
https://github.com/SalasLab/HiTIMED
Software DNA methylation-based algorithm, to estimate cell proportions in tumor microenvironment. Profiles tumor, immune, and angiogenic components, allowing researchers to study tumor composition and its clinical implications using archival biospecimens.
Proper citation: HiTIMED (RRID:SCR_028180) Copy
https://github.com/brentp/somalier
Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches.
Proper citation: somalier (RRID:SCR_028167) Copy
Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles.
Proper citation: Natural Products Atlas (RRID:SCR_025107) Copy
https://pvactools.readthedocs.io/en/latest/
Software toolkit to identify and visualize cancer neoantigens. Cancer immunotherapy tools suite consisting of following tools: pVACseq as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from VCF file; pVACbind as cancer immunotherapy pipeline for identifying and prioritizing neoantigens from FASTA file; pVACfuse as tool for detecting neoantigens resulting from gene fusions; pVACvector as tool designed to aid specifically in construction of DNA-based cancer vaccines; pVACview as application based on R Shiny that assists users in reviewing, exploring and prioritizing neoantigens from results of pVACtools processes for personalized cancer vaccine design.
Proper citation: pVACtools (RRID:SCR_025435) Copy
http://www.bios.unc.edu/research/genomic_software/Matrix_eQTL/
Software tool for ultra fast eQTL analysis via large matrix operations.
Proper citation: MatrixEQTL (RRID:SCR_025513) Copy
Software quality assurance and checking tool for quantitative assessment of magnetic resonance imaging and computed tomography data. Used for quality control of MR imaging data.
Proper citation: MRQy (RRID:SCR_025779) Copy
https://github.com/kbolton-lab/ArCH
Software somatic variant calling pipeline designed to detect low variant allele fraction clonal hematopoiesjsonsis variants.
Proper citation: ArCH (RRID:SCR_025975) Copy
https://www.bioconductor.org/packages/release/bioc/html/methylSig.html
Software R package as whole genome DNA methylation analysis pipeline. Used for testing differentially methylated cytosines or regions in whole-genome bisulfite sequencing or reduced representation bisulfite sequencing experiments. Several options exist for either site-specific or sliding window tests, and variance estimation.
Proper citation: MethylSig (RRID:SCR_025849) Copy
https://spatialge.moffitt.org/
Web application, a user friendly, point-and-click implementation of spatialGE R package. Contains collection of methods for visualization and spatial statistics analysis of tissue microenvironment and heterogeneity using spatial transcriptomics experiments. Used for user-friendly analysis of spatial transcriptomics data.
Proper citation: Moffitt spatialGE (RRID:SCR_025980) Copy
https://www.unmc.edu/vcr/cores/vcr-cores/confocal-microscopy/index.html
Facility houses imaging technologies ranging from super resolution (~ 0.120 um to 0.020 um) to microscopic (~ 0.300 um) to mesoscopic (~ 1 um) biomedical imaging. Imaging specialists provide training and/or actively assist researchers collecting images across imaging instrumentation. Instrumentation includes Zeiss ELYRA PS.1 is inverted microscope for super resolution (SR) structured illumination microscopy (SIM) and single molecule localization microscopy (SMLM) including, PhotoActivated Localization Microscopy (PALM) using photo switchable/convertible fluorescent proteins, Total Internal Reflection Fluorescence (TIRF) and STochastic Optical Reconstruction Microscopy (STORM);Zeiss 800 CLSM with Airyscan is an inverted microscope dramatically increasing conventional confocal image resolution to ~180 nm using Airyscan technology; Zeiss 710 LSM is inverted microscope supporting most basic imaging applications, multi channel and spectral, co localization, live cell, 3D, and time series imaging; Zeiss Celldiscoverer 7 is widefield imaging system for automated, time lapse imaging of live samples; Zeiss Axioscan 7 is high performance whole slide scanning system for fluorescence, brightfield, and polarization imaging;Miltenyi Biotec Ultramicroscope II Light Sheet fluorescence microscope (LSFM) extends fluorescent imaging into true 3D, large scale volumetric imaging of intact tissues, organs, and small organisms. AMCF also houses several high-end data analysis workstations with premier image analysis software including HALO (Indica Labs) and IMARIS (Oxford Instruments) facilitating data rendering, analyses, and presentation options.
Proper citation: University of Nebraska Medical Center Advanced Microscopy Core Facility (RRID:SCR_022467) Copy
https://www.utsouthwestern.edu/labs/qlmc/
Provides access to variety of microscope modalities including laser scanning and spinning disk confocal, multiphoton, wide field deconvolution, CFP/YFP FRET, TIRF, single molecule imaging, and more. Offers customized microscopy training, advise and help with sample preparation, image quantification, and offer basic microscope maintenance. Can streamline your data handling and image visualization as well as automate your image analysis workflow through customized Fiji macros.
Proper citation: University of Texas Southwestern Medical Center Quantitative Light Microscopy Core Facility (RRID:SCR_022605) Copy
https://www.nationwidechildrens.org/research/areas-of-research/biopathology-center/about
Provides services related to biospecimen procurement, banking, processing, and distribution. Housed biospecimen collections are from biorepositories of National Cancer Institute funded Children’s Oncology Group, NRG Oncology-Columbus (formerly the GOG Tissue Bank), SWOG, Pediatric Division of Cooperative Human Tissue Network, and Biospecimen Core Resource of Center for Cancer Genomics, as well as numerous biospecimen collections sponsored by funded NCH investigators. Cooperative Human Tissue Network is one of six institutions funded by National Cancer Institutes to access to remnant human tissues for biomedical researchers throughout the United States and Canada. Offers expertise in tissue preparation and preservation to meet the research needs of basic and applied scientists.
Proper citation: Nationwide Children’s Hospital Abigail Wexner Research Institute Biopathology Center Core Facility (RRID:SCR_023260) Copy
https://health.ucdavis.edu/cancer/research/sharedresources/biostatistics.html
Provides expertise in design, analysis and reporting of cancer related studies, including basic, translational, clinical and population based research. BSR affiliated faculty and staff work with investigators from the earliest stages of study planning. The shared resource is especially committed to mentoring early career cancer researchers.
Proper citation: University of California Davis Health Biostatistics Shared Resource Core Facility (RRID:SCR_023585) Copy
https://health.ucdavis.edu/cancer/research/sharedresources/combichem.html
Provides high throughput screening platform to discover unique chemical probes against biological targets using various one bead one compound and one bead two compound combinatorial libraries.Interacts closely with resource users on optimization of the lead compounds via focused libraries and standard medicinal chemistry techniques. Provides custom synthesis of telodendrimer based micellar nanoparticle platform for efficient drug delivery.
Proper citation: University of California Davis Health Combinatorial Chemistry and Chemical Biology Shared Resource Core Facility (RRID:SCR_023584) Copy
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the RRID Resources search. From here you can search through a compilation of resources used by RRID and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that RRID has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on RRID then you can log in from here to get additional features in RRID such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
You can save any searches you perform for quick access to later from here.
We recognized your search term and included synonyms and inferred terms along side your term to help get the data you are looking for.
If you are logged into RRID you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the sources that were queried against in your search that you can investigate further.
Here are the categories present within RRID that you can filter your data on
Here are the subcategories present within this category that you can filter your data on
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
