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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.
Web app that allows users to search for the most important paths connecting any two nodes in Hetionet.
Proper citation: Hetnet Connectivity Search (RRID:SCR_023630) Copy
Web server application that infers overrepresentation of upstream kinases whose putative substrates are in user inputted list of proteins. Used to analyze data from phosphoproteomics and proteomics studies to predict upstream kinases responsible for observed differential phosphorylations.
Proper citation: Kinase Enrichment Analysis 3 (RRID:SCR_023623) Copy
https://generanger.maayanlab.cloud/gene/A2M?database=ARCHS4
Web server application that provides access to processed data about expression of human genes and proteins across human cell types, tissues, and cell lines from several atlases. Used to explore single gene expression across tissues and cell types.
Proper citation: GeneRanger (RRID:SCR_023622) Copy
https://targetranger.maayanlab.cloud/
Web server application that identifies targets from user inputted RNA-seq samples collected from cells we wish to target. By comparing inputted samples with processed RNA-seq and proteomics data from several atlases, TargetRanger identifies genes that are highly expressed in target cells while lowly expressed across normal human cell types, tissues, and cell lines.
Proper citation: TargetRanger (RRID:SCR_023621) Copy
Medical wiki of interventions, regimens, and general information relevant to fields of hematology and oncology. Knowledge base for hematology and oncology providers, containing details about hematology/oncology drugs and treatment regimens. Any healthcare professional can sign up to contribute. Acuracy and completeness of content is overseen by Editorial Board.
Proper citation: HemOnc Knowledgebase (RRID:SCR_023436) Copy
https://github.com/JamieHeather/stitchr
Software Python tool for stitching coding T cell receptors nucleotide sequences from V,J,CDR3 information. Produces complete coding sequences representing fully spliced TCR cDNA given minimal V,J,CDR3 information.
Proper citation: Stitchr (RRID:SCR_022139) Copy
http://cancer.gov/cancertopics/pdq/cancerdatabase
NCI''s comprehensive cancer database that contains summaries on a wide range of cancer topics; a registry of 8,000+ open and 19,000+ closed cancer clinical trials from around the world; a directory of professionals who provide genetics services; the NCI Dictionary of Cancer Terms, with definitions for 6,800+ cancer and medical terms; and the NCI Drug Dictionary, which has information on 2,300+ agents used in the treatment of cancer or cancer-related conditions. The PDQ cancer information summaries are peer reviewed and updated monthly by six editorial boards comprised of specialists in adult treatment, pediatric treatment, supportive care, screening and prevention, genetics, and complementary and alternative medicine. The Boards review current literature from more than 70 biomedical journals, evaluate its relevance, and synthesize it into clear summaries. Many of the summaries are also available in Spanish.
Proper citation: Physician Data Query (RRID:SCR_006833) Copy
A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.
Proper citation: Synapse (RRID:SCR_006307) Copy
https://ccb.jhu.edu/software/stringtie/
Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ .
Proper citation: StringTie (RRID:SCR_016323) Copy
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
Proper citation: DESeq2 (RRID:SCR_015687) Copy
https://www.rdocumentation.org/packages/DGCA/versions/1.0.2
Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix.
Proper citation: Differential Gene Correlation Analysis (RRID:SCR_020964) Copy
http://statistika.mfub.bg.ac.rs/interactive-linegraph/
Interactive web based tool for creating line graphs for scientific publications. Users can view different summary statistics, examine lines for any individual in data, focus on time points or groups of interest, and view changes between any two time points and conditions.
Proper citation: Interactive Line Graph (RRID:SCR_018334) Copy
https://cadd.gs.washington.edu/
Web tool for predicting deleteriousness of variants throughout human genome. Software tool for scoring deleteriousness of single nucleotide variants as well as insertion and deletions variants in human genome.
Proper citation: Combined Annotation Dependent Depletion (RRID:SCR_018393) Copy
https://geodacenter.github.io/
Software program for spatial analysis for non geographic information systems specialists. Includes functionality ranging from simple mapping to exploratory data analysis, visualization of global and local spatial autocorrelation, and spatial regression.
Proper citation: GeoDa (RRID:SCR_018559) Copy
https://www.mskcc.org/research/ski/core-facilities/monoclonal-antibody-core-facility
ABCF can provide MAbs from established hybridomas for RESEARCH PURPOSES ONLY, can assist in generating MAbs, offers a weekly mycoplasmal contamination screening service for tissue culture samples, distributes cell lines developed at Memorial Sloan Kettering Cancer Center and Rockefeller University.
Proper citation: Memorial Sloan Kettering Cancer Center Antibody and Bioresource Core Facility (RRID:SCR_017691) Copy
Core mass spec and proteomic services include open access lab for trained users with GC/MS, LC/MS, high resolution LC/MS, and MALDI-TOF instruments, help with intact protein analysis, targeted quantitation, drug discovery support, pathway analysis, protein interactions, FFPE tissue analysis, both labeled and label-free proteomics, and more. Please contact SUMS to discuss these and other custom projects including new application development.
Proper citation: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility (RRID:SCR_017801) Copy
http://rhlccflow.facilities.northwestern.edu
Provides 6 cell sorters and 5 benchtop analyzers. Helps investigators to define their projects in the early stages of development to make optimal and efficient use of flow cytometry. Educates ALL users (faculty and staff) in the science and technology of flow cytometry.
Proper citation: Northwestern University Cancer Center Flow Cytometry Core Facility (RRID:SCR_017766) Copy
http://cancer.northwestern.edu/research/shared-resources/pathology-core-facility.html
Centralized, comprehensive, core laboratory providing histology, immunohistochemistry, molecular analysis and extraction and microscopic evaluation services for human tissue-based studies. Serves integral marker studies that require biomarker-based treatment arm assignment. Performs procurement of fresh biospecimens for clinical trials and biobanking.
Proper citation: Northwestern University School of Medicine Lurie Cancer Center Pathology Core Facility (RRID:SCR_017769) Copy
https://med.nyu.edu/research/scientific-cores-shared-resources/proteomics-laboratory
Core offers specialized expertise for analysis of proteins and peptides using mass spectrometry. Develops new methods and customized approaches for proteomic analysis and suggests experimental strategies and sample preparation prior to mass spectrometry analysis. Services include:comprehensive protein identification ,analysis of affinity purified complexes,characterizing protein post-translational modifications,de novo sequencing,label and label-free quantitation ,multiplexed quantitation global phosphorylation and ubiquitin analysis,analysis of laser-capture microdissected formalin-fixed paraffin-embedded tissue,secretome analysis,crosslinking analysis,disulfide mapping.
Proper citation: New York University School of Medicine Langone Health Proteomics Laboratory Core Facility (RRID:SCR_017926) Copy
https://isairr.bsd.uchicago.edu/
Core offers imaging modalities, techniques, and services for in vivo imaging of small animals and ex vivo imaging of tissue/organ specimens. iSAIRR sub-cores feature magnetic resonance imaging and spectroscopy (MRIS); optical imaging (bioluminescence and fluorescence); positron emission tomography, single photon emission computed tomography, and computed tomography (PET/SPECT/CT).Services include Assistance with experimental design,Assisted and/or independent image acquisition,Veterinary support for all imaging modalities,Assistance with data processing and interpretation.
Proper citation: Chicago University Integrated Small Animal Imaging Research Resource Core Facility (RRID:SCR_017923) Copy
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