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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/theislab/scvelo

Software package for estimating and analyzing RNA velocities in single cells using dynamical modeling. RNA Velocity using dynamical modeling.

Proper citation: scVelo (RRID:SCR_018168) 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

http://rloop.bii.a-star.edu.sg/?pg=qmrlfs-finder

A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis.

Proper citation: QmRLFS-finder (RRID:SCR_014584) Copy   

•   Source: SciCrunch Registry

https://github.com/DiogoVeiga/maser

Software package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events. Mapping alternative splicing events to proteins.

Proper citation: maser (RRID:SCR_023484) 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.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

http://digestivediseasescenters.org/content/ddrc-emory-university-overview

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th, 2023. Core facility for the Emory Epithelial Pathobiology Research Development Center.

Proper citation: Emory Epithelial Pathobiology Research Development Center Image Analysis Core (RRID:SCR_015917) Copy   

•   Source: SciCrunch Registry

https://sdrc.stanford.edu/sdrc-research-cores/dgac/home/

Core facility that offers library preparation and sequencing services on a variety of platforms - Illumina HiSeq 4000, MiSeq, HiSeq 2500 and PacBio Sequel - as well as bioinformatics analysis. It can sequence a variety of commercial sample preparation kits as well as custom workflows. DGAC provides access to high throughput sequencing and analysis to researchers at the Stanford Diabetes Research Center.

Proper citation: Stanford Diabetes Research Center Diabetes Genomics Analysis Core (RRID:SCR_016213) Copy   

•   Source: SciCrunch Registry

https://www.hpc.cam.ac.uk/compbio

Provides assistance in characterization and analysis of genomic variants, next generation sequencing data processing and analysis, computational systems biology, HPC and big data software development for genome scale data analysis, machine learning and data mining, cloud based solutions to process and manage large amounts of data, databases and genome scale data visualization.

Proper citation: University of Cambridge Bioinformatics and Computational Biology Services Core Facility (RRID:SCR_017154) Copy   

•   Source: SciCrunch Registry

http://rrc.uic.edu/cores/scientific-imaging-nanotechnology/electron-microscopy-service-ems/

Core provides electron microscopy imaging and analytical characterization, surface analysis by XPS or Raman, access to instrumentation, training, and service for using scanning (SEM), transmission (TEM) and scanning transmission (STEM) electron microscopy, surface analysis and vibrational spectroscopy, specimen preparation.

Proper citation: University of Illinois at Chicago Electron Microscopy Core Facility (RRID:SCR_017763) Copy   

•   Source: SciCrunch Registry

http://www.feinberg.northwestern.edu/research/cores/units/clin-pharm.html

Core provides quantitative mass spectrometry based support for in vitro studies and both preclinical and clinical studies of variety of small molecules, including cancer chemotherapeutic agents, analgesics, and antidepressants. Expertise includes optimizing design, conduct, analysis, interpretation, and reportage of pharmacokinetic studies. Helps with biological sample preparation, quantitative mass spectrometric drug concentration measurement, and drug concentration versus time data modeling. Small molecule concentrations in plasma and other body fluids are measured using Sciex 6500 QTrap with UPLC and nano LC or an Agilent HPLC system linked to Applied Biosystems API 3000 triple quadrupole mass spectrometer after sample preparation by, for example, solid-phase extraction. Drug concentration versus time relationships are fitted to various compartmental pharmacokinetic models using commercially available and specialized software.

Proper citation: Northwestern University Mary Beth Donnelley Clinical Pharmacology Core Facility (RRID:SCR_017768) Copy   

•   Source: SciCrunch Registry

https://www.bif.northwestern.edu/

Shared use and training facility. Servies include Confocal Laser Scanning Microscopy, DIC (Differential Interference Contrast Microscopy), FCS (Fluorescence Correlation Spectroscopy), FLIP (Fluorescence-Loss-In-Photobleaching), FRAP (Fluorescence Recovery After Photobleaching),FRET (Fluorescence/ Forster Resonance Energy Transfer),Live-cell Imaging,Phase Contrast Microscopy,Widefield Fluorescence Microscopy,Image Processing and Analysis. Services include poster printing, and specimen preparation. Provides training for most instruments. Instruments include Leica DM6B Fluorescent Microscope (Hogan 5-112), Leica TCS SP8 Confocal Microscope (Hogan 5-128),Leica SP5 II Confocal Microscope (Hogan 5-114),Leica Spinning Disk Confocal Microscope (Hogan 5-113),DeltaVision Deconvolution Microscope (Hogan 5-111),Olympus IX83 Inverted Fluorescent Microscope (Silverman Hall 1-567),Olympus IX53 Inverted Color Microscope (Silverman Hall 1-567), LionHeart Automated Microscope BioTeck (Hogan 5-110).

Proper citation: Northwestern University Biological Imaging Core Facility (RRID:SCR_017767) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://nationalmaglab.org/user-facilities/icr

Facility provides service operations for sample analysis that requires ultrahigh resolution and high mass accuracy of Fourier Transform Ion Cyclotron Resonance. Used for research in biomolecular analysis, hydrogen-deuterium exchange and environmental and petrochemical analysis. Four FT-ICR mass spectrometers feature high magnetic fields including the world-record 21 tesla and are compatible with multiple ionization and fragmentation techniques.

Proper citation: National High Magnetic Field Laboratory Ion Cyclotron Resonance Core Facility (RRID:SCR_017361) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://biology.hunter.cuny.edu/index.php?option=com_content&view=article&id=44&Itemid=62

Core provides access to instruments, ranging from simple white light wide field microscopes to fluorescent multidimensional super resolution and confocal imaging systems. Provides expertise in areas of microscopy including laser scanning confocal microscopy, super resolution microscopy, two photon microscopy. Helps with image analysis software packages, including, Imaris, Volocity, Autoquant, MetaMorph, and NIS-Elements.

Proper citation: Hunter College Digital Bio-Imaging Core Facility (RRID:SCR_017774) Copy   

•   Source: SciCrunch Registry