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https://maayanlab.cloud/drugmonizome/#/

Database with search engine for querying annotated sets of drugs and small molecules for performing drug set enrichment analysis.

Proper citation: Drugmonizome (RRID:SCR_024821) Copy   

•   Source: SciCrunch Registry

https://nprc.org/

NPRC Consortium is collaboration across seven Centers to increase access and promote sharing of NonHuman Primate related resources among biomedical researchers. NPRCs advance missions of NIH Institutes, Centers, and Offices by providing animals, facilities, expertise, and resources required by investigators in disease specific areas. Each Center provides expertise on the use of various NHP species as models of human disease to address specific research projects in major research fields such as infectious diseases, aging, cardiovascular disease, diabetes and metabolic disorders, neuroscience, pediatrics, regenerative medicine, reproductive health, and women’s health. ORIP supports Specific Pathogen Free rhesus macaque colonies at the California,Oregon, Southwest, Yerkes, and Tulane NPRCs and the Caribbean Primate Research Center in Puerto Rico. Additionally, SPF pigtail macaque colonies are maintained at the Washington NPRC and at the Johns Hopkins University School of Medicine.

Proper citation: National Primate Research Center Consortium (RRID:SCR_024839) Copy   

•   Source: SciCrunch Registry

https://github.com/nlm-irp-jianglab/SpikeHunter

Software deep learning tool for identifying phage tailspike proteins. Used to identify phage tailspike proteins.

Proper citation: SpikeHunter (RRID:SCR_024831) Copy   

•   Source: SciCrunch Registry

https://github.com/bpucker/NAVIP

Software tool for functional impact prediction for sequence variants. Neighborhood-Aware Variant Impact Predictor (NAVIP) considers all variants within a given protein coding sequence when predicting the functional consequences.

Proper citation: NAVIP (RRID:SCR_024838) Copy   

•   Source: SciCrunch Registry

https://pephub.databio.org

Web biological metadata server to view, store, and share your sample metadata in form of Portable Encapsulated Projects. PEPhub takes advantage of PEP biological metadata standard to store, edit, and access your PEPs in one place. Components include database where PEPs are stored; API to programmatically read and write PEPs in database; web based user interface to view and manage these PEPs via front end.

Proper citation: PEPhub (RRID:SCR_024892) Copy   

•   Source: SciCrunch Registry

https://cellxgene.cziscience.com/

Portal used to find and download any of data sets published on CELLxGENE. Allows to download and visually explore data to understand functionality of human tissues at cellular level. Optimized for finding, exploring, and reusing single cell data. Collections Page lists collections hosted on CELLxGENE Discover and metadata that define tissue, assay, disease, organism, and cell count for each collection. Once you find published dataset of interest on CELLxGENE Discover, you can click on the explore button below the dataset description to explore the cells of that dataset using the CELLxGENE Explorer.

Proper citation: CZ CELLxGENE Discover (RRID:SCR_024894) Copy   

•   Source: SciCrunch Registry

https://research.lsuhs.edu/cores/research-core-facilities

Core provides access to research services, educational and training opportunities, and technologies including cellular metabolism, flow cytometry, fluorescence, confocal, super resolution confocal microscopy, next generation sequencing, and real-time PCR. Provides assistance with all aspects of these technologies, including experimental design, protocol optimization, instrument operation, and data analysis.

Proper citation: Louisiana State University in Shreveport Research Core Facility (RRID:SCR_024775) Copy   

•   Source: SciCrunch Registry

https://wonder.cdc.gov/cancer.html

United States Cancer Statistics public information data provided by Centers for Disease Control and Prevention.

Proper citation: United States Cancer Statistics Public Information Data (RRID:SCR_024896) Copy   

•   Source: SciCrunch Registry

https://resources.aertslab.org/cistarget/

Web application to download database for motif enrichment, motif annotations,cluster-buster implementation, precomputed regions for creating gene-based databases and to download lists of transcription factors for human, mouse and fly, chip-seq tracks annotations.

Proper citation: cisTarget (RRID:SCR_024808) Copy   

•   Source: SciCrunch Registry

https://github.com/xjtu-omics/msisensor-pro

Software tool for microsatellite instability detection using high throughput sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region sequencing data as input. Introduces multinomial distribution model to quantify polymerase slippages for each tumor sample and discriminative sites selection method to enable MSI detection without matched normal samples.

Proper citation: MSIsensor-pro (RRID:SCR_024765) Copy   

•   Source: SciCrunch Registry

https://www.adobe.com/ca/products/fresco.html

Software digital painting and drawing application. Used to create figures. Built for the latest stylus and touch devices, now including iPhones. Collection of vector and raster brushes, live brushes, to deliver natural painting and drawing experience.Vector and raster graphics editor developed by Adobe primarily for digital painting. Originally designed for the Apple iPad with Pencil support.

Proper citation: Adobe Fresco (RRID:SCR_024887) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FAST

Software tool to segment 3D image of brain into different tissue types like Grey Matter, White Matter, CSF, etc., whilst also correcting for spatial intensity variations also known as bias field or RF inhomogeneities. Used to perform tissue type segmentation and bias field correction.

Proper citation: FMRIB's Automated Segmentation Tool (RRID:SCR_024920) Copy   

•   Source: SciCrunch Registry

https://github.com/broadinstitute/ichorCNA

Software tool that quantifies tumor content in cfDNA from 0.1× coverage whole-genome sequencing data without prior knowledge of tumor mutations. Used to simultaneously segment genome, predict large scale copy number alterations, and estimate tumor fraction of ultra low pass whole genome sequencing sample.

Proper citation: ichorCNA (RRID:SCR_024768) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT

Sotware automated robust and accurate tool for linear (affine) intra- and inter-modal brain image registration.

Proper citation: FMRIB's Linear Image Registration Tool (RRID:SCR_024922) Copy   

•   Source: SciCrunch Registry

https://github.com/hetio/xswap

Software Python library (C++ backend) for degree preserving network randomization.

Proper citation: XSwap (RRID:SCR_024802) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FNIRT

Software tool to perform linear registration, meaning that it will translate, rotate, zoom and shear one image to match it with another.

Proper citation: FNIRT (RRID:SCR_024923) Copy   

•   Source: SciCrunch Registry

https://github.com/STOmics/SGAE

Software graph neural network based tool for spatial domain deciphering. Used for deciphering spatial domains from spatially resolved transcriptomics.

Proper citation: SGAE (RRID:SCR_024803) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/SIENA

Software package for both single-time-point and two-time-point analysis of brain change. Used to estimate percentage brain volume change between two input images, taken of the same subject, at different points in time.

Proper citation: SIENA (RRID:SCR_024925) Copy   

•   Source: SciCrunch Registry

https://noncodingrna.org/detection-unit/

Detection Unit of ncRNA Core can perform highly sensitive microRNA detection platform for diverse biospecimens.Technology is based on qPCR and uses single plate panel for simultaneous detection of 384 miRNAs using MIRXES technology. Services offered by unit include Detection of miRNA, Analysis of dysregulated miRNA,Consultation and support for non-coding RNA biology and research.

Proper citation: Beth Israel Deaconess Medical Center Precision RNA Medicine Detection Unit Core Facility, (RRID:SCR_024819) Copy   

•   Source: SciCrunch Registry

https://research.lsuhs.edu/cores/research-core-facilities/small-animal-imaging-facility

Core provides imaging support to investigators who use small animal models in their research. Offers bioluminescence and fluorescence imaging, X-ray imaging, computed tomography, and positron emission tomography. Core provides imaging support services for investigators, including assistance in experimental design, conducting animal studies including anesthetization and imaging acquisition, and processing and interpreting imaging data.

Proper citation: Louisiana State University in Shreveport Small Animal Imaging Core Facility (RRID:SCR_024777) Copy   

•   Source: SciCrunch Registry