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http://amp.pharm.mssm.edu/X2K/

Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures.

Proper citation: eXpression2Kinases (RRID:SCR_016307) Copy   

•   Source: SciCrunch Registry

https://metasystems-international.com/us/products/metafer/

Software application to control the slide scanning hardware in Metasystem scanning and imaging platform used for automated image analysis applications in cytogenetics, hematology, pathology, toxicology, forensic sciences or microbiology microscopy. Optimized for clinical routine.

Proper citation: Metafer (RRID:SCR_016306) Copy   

•   Source: SciCrunch Registry

https://cibersort.stanford.edu/

Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.

Proper citation: CIBERSORT (RRID:SCR_016955) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/neurolucida-explorer

Companion analytical software for Neurolucida and Neurolucida 360, designed to perform extensive morphometric analysis on neuron reconstructions, serial section reconstructions, and brain maps.

Proper citation: Neurolucida Explorer (RRID:SCR_017348) Copy   

•   Source: SciCrunch Registry

https://github.com/sccn/labstreaminglayer

System for unified collection of measurement time series in research experiments that handles networking, time synchronization, near real time access as well as optionally centralized collection, viewing and disk recording of data. System for synchronizing streaming data for live analysis or recording.

Proper citation: Lab Streaming Layer (RRID:SCR_017631) Copy   

•   Source: SciCrunch Registry

https://github.com/AllenInstitute/scrattch.hicat

Software R package as hierarchical, iterative clustering for analysis of transcriptomics data.Used for single cell RNA-seq analysis for transcriptomic type characterization from Allen Institute.

Proper citation: Scrattch.Hicat (RRID:SCR_018099) Copy   

•   Source: SciCrunch Registry

https://qgis.org/en/site/

Open source cross platform desktop geographic information system application that supports viewing, editing, and analysis of geospatial data. Functions as geographic information system software, allowing users to analyze and edit spatial information, in addition to composing and exporting graphical maps.

Proper citation: QGIS (RRID:SCR_018507) Copy   

•   Source: SciCrunch Registry

https://github.com/cobilab/altair

Software C toolkit for alignment free and spatial temporal analysis of multi-FASTA data. Used for entangling presence of multiple sequences from epidemic and pandemic events.

Proper citation: AltaiR (RRID:SCR_024752) Copy   

•   Source: SciCrunch Registry

https://ensigna.com/

Contract research organization based in San Leandro, California, that specializes in molecular pathology, genomics, and tissue analysis. Services for drug discovery, biomarker development, and personalized medicine. Provides histopathology and genomic services to the pharmaceutical and biotechnology industries.

Proper citation: Ensigna Biosystems (RRID:SCR_028450) Copy   

•   Source: SciCrunch Registry

https://ag.purdue.edu/researchservices/

ARGE Research Services is dedicated to empowering Purdue Agriculture research by providing expert solutions in conducting team science, implementing best practices for data acquisition, stewardship, and analysis.

Proper citation: Purdue University College of Agriculture Research Services Core Facility (RRID:SCR_027377) Copy   

•   Source: SciCrunch Registry

https://qipcm.com/

Provides testing and analysis support for clinical trials to improve consistency and reliability in clinical trial data.Helps clinical investigators achieve systematic image collection and improved collaboration. Can help with handling large volume functional and dynamic imaging data.

Proper citation: University Health Network Quantitative Imaging for Personalized Cancer Medicine Advanced Imaging Core Facility (RRID:SCR_027527) Copy   

•   Source: SciCrunch Registry

https://www.ladydavis.ca/en/about/core-facilities/flow-cytometry/

Core provides complete flow cytometry analysis and cell sorting services in terms of experimental design, instrumentation, training, technical assistance and scientific guidance from sample preparation to publication.

Proper citation: Lady Davis Institute Flow Cytometry Core Facility (RRID:SCR_027644) Copy   

•   Source: SciCrunch Registry

https://www.mskcc.org/research/ski/core-facilities/research-pharmacy

Core is a full-service facility that prepares agents developed by MSK researchers to be used as investigational drugs in preclinical or clinical studies. The Core comprises three principal groups: the Pharmaceutical Product Facility (PPF) for drug formulation/stability and preparation; the Clinical Grade Production (CGP) Facility for bulk product manufacturing, purification, and vialing; and the Pharmacy Investigational Drug Service (PIDS), which develops, procures, prepares, and validates the preparation, packaging, and distribution of investigational drugs for clinical use. Core services include: formulation, analysis, and evaluation of drug release rates; prediction of interactions; and determinations of compatibility and physical stability of medications. Based on the expertise of the RP Core, MSK has been able to bring into early-phase clinical trials multiple types of pharmacologic agents, including traditional small molecules, radiopharmaceuticals, and vaccines.

Proper citation: Memorial Sloan Kettering Cancer Center Research Pharmacy Core Facility (RRID:SCR_027807) Copy   

•   Source: SciCrunch Registry

https://github.com/csitron/Amino_acid_composition_and_hydrophobicity_analysis

Software package to analyze amino acid content and hydrophobicity profile of given set of protein sequences in fasta file. Used for analysis of amino acid composition and hydrophobicity of test sequences from fasta files.

Proper citation: Amino_acid_composition_and_hydrophobicity_analysis (RRID:SCR_026281) Copy   

•   Source: SciCrunch Registry

http://tuskegee.eagle-i.net/i/00000136-648c-c32f-ee37-018280000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 30,2023. Core provides services and training in computational biology, bioinformatics, experimental design and statistical analysis to the RCMI researchers and the biomedical research community at Tuskegee University.

Proper citation: Tuskegee University Computational Biology and Bioinformatics - Biomedical Information Management Services (RRID:SCR_010065) Copy   

•   Source: SciCrunch Registry

http://www.esri.com/software/arcgis/arcgis-for-desktop

Geographical information system software produced by Esri.

Proper citation: ArcGIS for Desktop Basic (RRID:SCR_011081) Copy   

•   Source: SciCrunch Registry

http://www.scienceexchange.com/facilities/dna-microarray-core-facility-ualbany

Core provides microarray services for Affymetrix GeneChip arrays, Agilent microarrays, NimbleGen microarrays and custom-produced spotted cDNA microarrays. Projects developed through DNA Microarray Center have made use of arrays from variety of genomes, eukaryotic, prokaryotic, and plant. Core services includes RNA/DNA isolation, gene expression, miRNA, Chip-chip, Rip-chip and DNA methylation services. Provides bioinformatics tools for further analysis of results of expression experiments.

Proper citation: University at Albany Center for Functional Genomics DNA Microarray Core Facility (RRID:SCR_012502) Copy   

•   Source: SciCrunch Registry

https://www.mcgill.ca/cian/

Core facility at Biology Department in McGill Faculty of Science. Expertise in Light Microscopy and Image Analysis. Provides light microscopes, ranging from Point Scanning and Spinning Disc Confocals to Multi-Photon, TIRF, Light Sheet and Super-Resolution microscopes. Provides services in Automation/High throughput screening (liquid handler, pinning robot), Protein expression and antibody production. Users get training.

Proper citation: McGill Cell Imaging and Analysis Network Core Facility (RRID:SCR_012623) Copy   

•   Source: SciCrunch Registry

http://diabetesresearch.med.umich.edu/Core_MCDTR_Methods.php

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on November 6,2024. Research core that works to assist investigators in designing studies, collecting data, and analyzing data to examine questions related to the causes, prevention, and control of diabetes, its complications, and comorbidities.

Proper citation: Michigan Center for Diabetes Translational Research Methods and Measurements Core (RRID:SCR_015188) Copy   

•   Source: SciCrunch Registry

http://www.github.com/kmuench/16p_resource

Software tool as a code to support figure generation for the manuscript by Roth, Muench et al. Used to perform analysis.

Proper citation: 16p_resource Code (RRID:SCR_016845) Copy   

•   Source: SciCrunch Registry