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https://signalingpathways.org

Web multi omics knowledgebase based upon public, manually curated transcriptomic and cistromic datasets involving genetic and small molecule manipulations of cellular receptors, enzymes and transcription factors. Integrated omics knowledgebase for mammalian cellular signaling pathways. Web browser interface was designed to accommodate numerous routine data mining strategies. Datasets are biocurated versions of publically archived datasets and are formatted according to recommendations of the FORCE11 Joint Declaration on Data Citation Principles73, and are made available under Creative Commons CC 3.0 BY license. Original datasets are available.

Proper citation: Signaling Pathways Project (RRID:SCR_018412) Copy   

•   Source: SciCrunch Registry

http://www.midasplatform.org/

Open-source toolkit that enables the rapid creation of tailored, web-enabled data storage and provides a cohesive system for data management, visualization, and processing. At its core, Midas Platform is implemented as a PHP modular framework with a backend database (PostGreSQL, MySQL and non-relational databases). While the Midas Platform system can be installed and deployed without any customization, the framework has been designed with customization in mind. As building one system to fit all is not optimal, the framework has been extended to support plugins and layouts. Through integration with a range of other open-source toolkits, applications, or internal proprietary workflows, Midas Platform offers a solid foundation to meet the needs of data-centric computing. Midas Platform provides a variety of data access methods, including web, file system and DICOM server interfaces, and facilitates extending the methods in which data is stored to other relational and non-relational databases.

Proper citation: Midas Platform (RRID:SCR_002186) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/whs-sd-atlas/

Open access volumetric atlas of anatomical delineations of rat brain based on structural contrast in isotropic magnetic resonance and diffusion tensor images acquired ex vivo from 80 day old male Sprague Dawley rat at Duke Center for In Vivo Microscopy. Spatial reference is provided by Waxholm Space coordinate system. Location of bregma and lambda are identified as anchors towards stereotaxic space. Application areas include localization of signal in non structural images. Atlas, MRI and DTI volumes, and diffusion tensor data are shared in NIfTI format.

Proper citation: Waxholm Space Atlas of the Sprague Dawley Rat Brain (RRID:SCR_017124) Copy   

•   Source: SciCrunch Registry

https://pharos.nih.gov/idg/index#

Database of ligands and diseases. Its goal is to develop a knowledge-base for the Druggable Genome (DG) in order to illuminate the uncharacterized and/or poorly annotated portion of the genome. DG, focusing on four of the most commonly drug-targeted protein families: G-protein-coupled receptors (GPCRs); nuclear receptors (NRs); ion channels (ICs); and kinases.

Proper citation: PHAROS (RRID:SCR_016258) Copy   

•   Source: SciCrunch Registry

http://hb.flatironinstitute.org/

Formerly known as GIANT (Genome-scale Integrated Analysis of gene Networks in Tissues), HumanBase applies machine learning algorithms to learn biological associations from massive genomic data collections. These integrative analyses reach beyond existing "biological knowledge" represented in the literature to identify novel, data-driven associations.

Proper citation: HumanBase (RRID:SCR_016145) Copy   

•   Source: SciCrunch Registry

http://software.broadinstitute.org/gsea/msigdb/index.jsp

Collection of annotated gene sets for use with Gene Set Enrichment Analysis (GSEA) software.

Proper citation: Molecular Signatures Database (RRID:SCR_016863) 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://proteogenomics.musc.edu/ma/arrayQuest.php?page=home&act=manage

A web-accessible program for the analysis of DNA microarray data. ArrayQuest is designed to apply any type of DNA microarray analysis program executable on a Linux system (i.e., Bioconductor statistical and graphical methods written in R as well as BioPerl and C++ based scripts) to DNA microarray data stored in the MUSC DNA Microarray Database, the Gene Expression Omnibus (GEO) or in a password protected private database uploaded to the center point server. ArrayQuest analyses are performed on a computer cluster.

Proper citation: ArrayQuest (RRID:SCR_010935) 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

https://lsom.uthscsa.edu/dcsa/research/cores-facilities/optical-imaging/

Service resource which makes imaging technology available to investigators on UTHSCSA campus and neighboring scientific community. Core Optical Imaging Facility offers access to technology for imaging of living cells, tissues, and animals, consultation, education and assistance regarding theory and application of optical imaging techniques, technical advice on specimen preparation techniques and probe selection.

Proper citation: Texas University Health Science Center at San Antonio Long School of Medicine Department of Cell Systems and Anatomy Optical Imaging Core Facility (RRID:SCR_012171) Copy   

•   Source: SciCrunch Registry

https://www.moffitt.org/research-science/shared-resources/tissue/

Biorepository resource with mission of proper collection, handling, processing and storage of irreplaceable biological specimens to support spectrum of related basic science, translational and clinical research. Provides expertise in nucleic acid extractions, quantification, aliquoting and quality assurance; liquid specimen centrifugation, processing and aliquoting; histological tissue processing, immunohistochemistry and tissue microarray microtomy; pathologist consultation services. Tissue Core operations are divided into four distinct pillars of service that work collaboratively to ensure specimen quality is maintained from procurement to preservation.

Proper citation: Moffitt Cancer Center Tissue Core Facility (RRID:SCR_012364) Copy   

•   Source: SciCrunch Registry

https://github.com/willtownes/glmpca

Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data.

Proper citation: glmpca (RRID:SCR_025517) Copy   

•   Source: SciCrunch Registry

https://discover.nci.nih.gov/rsconnect/cellminercdb/

Web application integrating cancer cell line pharmacogenomics. Enables exploration and analysis of cancer cell line pharmacogenomic data across different sources. Focuses on cancer patient-derived human cell line molecular and pharmacological data. CellMinerCDB (v1.2) includes several improvements.

Proper citation: CellMinerCDB (RRID:SCR_025649) Copy   

•   Source: SciCrunch Registry

https://www.borch.dev/uploads/screpertoire/

Software R toolkit for analyzing single-cell immune repertoire profiling. Used for single-cell immune receptor analysis.

Proper citation: scRepertoire (RRID:SCR_025691) Copy   

•   Source: SciCrunch Registry

https://github.com/hms-dbmi/UpSetR

Software R package for visualization of intersecting sets and their properties.

Proper citation: UpSetR (RRID:SCR_026112) Copy   

•   Source: SciCrunch Registry

https://github.com/NCI-CGR/PLP_prediction_workflow/tree/autogvp

Software tool integrates ClinVar variant annotation with modified InterVar classification approach, based on American College of Medical Genetics-Association for Molecular Pathology guidelines, to output germline variant classification. Since AutoGVP input only requires VCF file, it can facilitate large-scale, clinically focused classification of germline sequence variants.

Proper citation: AutoGVP (RRID:SCR_026107) Copy   

•   Source: SciCrunch Registry

https://github.com/czc/nb_distribution

Software tool to discover somatic and germline structural variation breakpoints in whole genome sequencing data. Can report accurate breakpoints of Deletions, Duplications, Inversions and Translocations. Designed for Illumina paired-end data. Local assembly for breakpoint detection in cancer genomes.

Proper citation: NovoBreak (RRID:SCR_026032) Copy   

•   Source: SciCrunch Registry

https://oncotree.mskcc.org/

Community-driven cancer classification platform encompassing rare and common cancers that provides clinically relevant and appropriately granular cancer classification for clinical decision support systems and oncology research. Cancer classification system for precision oncology.

Proper citation: OncoTree (RRID:SCR_026218) Copy   

•   Source: SciCrunch Registry

https://genie.cbioportal.org/

International data-sharing consortium focused on generating an evidence base for precision cancer medicine by integrating clinical-grade cancer genomic data with clinical outcome data of cancer patients treated at multiple institutions worldwide.

Proper citation: AACR GENIE cBioPortal (RRID:SCR_026217) Copy   

•   Source: SciCrunch Registry

https://github.com/katerinakazantseva/strainy

Software tool for phasing and assembly of bacterial strains from long-read sequencing data (either Oxford Nanopore or PacBio). Given reference (or collapsed de novo assembly) and set of aligned reads as input, tool produces multi-allelic phasing, individual strain haplotypes and strain-specific variant calls. Used for phasing and assembly of strain haplotypes from long-read metagenome sequencing.

Proper citation: Strainy (RRID:SCR_026430) Copy   

•   Source: SciCrunch Registry