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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.
Software tool as data and metadata repository of Extracellular RNA Communication Consortium. Atlas includes small RNA sequencing and qPCR derived exRNA profiles from human and mouse biofluids. All RNAseq datasets are processed using version 4 of exceRpt small RNAseq pipeline. Atlas accepts submissions for RNAseq or qPCR data.
Proper citation: exRNA Atlas (RRID:SCR_017221) Copy
https://www.hsph.harvard.edu/hmac/
Core assists with consultation for microbiome project development, provides validated meta omic analysis of microbial community data, and supports fully collaborative grant funded investigations.
Proper citation: Harvard School of Public Health Microbiome Analysis Core Facility (RRID:SCR_017187) Copy
https://github.com/ZSI-Bio/bdg-sequila
Software tool for genomic intervals querying and processing built on top of Apache Spark. Elastic, fast and scalable SQL oriented solution for processing and querying genomic intervals.
Proper citation: SeQuiLa (RRID:SCR_017220) Copy
https://github.com/csbbcompbio/CSBB-v3.0
Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments.
Proper citation: Computational Suite for Bioinformaticians and Biologists (RRID:SCR_017234) Copy
Core facility for cystic fibrosis mouse strains. Services include mouse production from current strains and creation of new strains, mouse strain maintenance, tissue acquisition, genotyping and treatment of mice with IACUC approved drugs to test potential therapies. Maintains centralized database that contains breeding history, phenotypes observed and experimental records of various CF mouse strains.
Proper citation: Case Western Reserve University Cystic Fibrosis Mouse Models Core (RRID:SCR_017238) Copy
https://t1dexchange.org/research/biobank/
Collection of biological samples linked to participant medical data from individuals living with type 1 diabetes. Unifies samples and data from eight different clinical studies related to type 1 diabetes.
Proper citation: T1D Exchange Biobank (RRID:SCR_017195) Copy
https://github.com/josephryan/matemaker
Software tool to make artificial mate pairs from long sequences for scaffolding.
Proper citation: matemaker (RRID:SCR_017199) Copy
http://www.open-ephys.org/pulsepal
Open source pulse train generator that allows users to create and trigger software defined trains of voltage pulses with high temporal precision. Generates precisely timed pulse sequences for use in research involving electrophysiology or psychophysics.
Proper citation: Open Ephys: Pulse Pal (RRID:SCR_017203) Copy
https://github.com/greenhouselab/Veta
Software suite of functions for EMG data visualization and processing. Open source Matlab toolbox for electromyography combined with transcranial magnetic stimulation. MATLAB toolbox for the collection, analysis, and visualization of EMG and TMS.
Proper citation: VETA (RRID:SCR_017201) Copy
https://www.agilent.com/cs/library/usermanuals/Public/G2505-90019_ScannerC_User.pdf
Microarray Scanner is part of microarray analysis solution from Agilent Technologies. Laser induced fluorescence scanner designed to read microarrays printed on standard slides. Measures fluorescence intensity of labeled sample nucleic acid bound to microarrays.
Proper citation: Agilent: G2565CA Microarray Scanner (RRID:SCR_017206) Copy
https://github.com/llawas/Rice_HxD_Recovery_Metabolomics
Software tool as source code used in analysis of GC MS data from rice samples. Workflow for statistical analysis of GC MS data from field grown rice collected during rewatering after exposure to combined drought and heat stress.
Proper citation: Rice_HxD_Recovery_Metabolomics (RRID:SCR_017204) Copy
Software for 3D reconstruction from serial slices. Used to create 3D model to analyse organs, tissues and cells, create photos and videos to help scientists in life science, biology and medicine, visualize, analyze and exploit information from serial slices and get accurate quantitative information from reconstructed 3D models.
Proper citation: BioViz3D (RRID:SCR_017162) Copy
https://www.cbrg.ox.ac.uk/cbrg/
Core provides bioinformatics training and analysis tools. Supports bioinformatics analysis at University of Oxford.
Proper citation: University of Oxford Computational Biology Research Group Core Facility (RRID:SCR_017166) Copy
https://www.plantsci.cam.ac.uk/bioinformatics
Core provides assistance in data analysis to support members of Plant Sciences.
Proper citation: University of Cambridge Department of Plant Sciences Bioinformatics Core Facility (RRID:SCR_017164) Copy
https://labs.gladstone.org/bioinformatics/index.html
Core provides consulting services, sequencing, data analysis, and programming assistance. Used for Experimental Design and Power Analysis Consultation, RNA-seq, ChIP-seq, ATAC-seq analysis, Statistics consulting, Variant calling, Data normalization across multiple projects, General programming, Custom Figures for publication, tutorials for learning common software tools.
Proper citation: UCSF Gladstone Institutes Bioinformatics Core Facility (RRID:SCR_017178) Copy
Software event based framework for processing and controlling data streams. Visual language designed for making software systems that require rich and rapid interaction with external world.
Proper citation: Bonsai (RRID:SCR_017218) Copy
http://rna.urmc.rochester.edu/RNAstructureWeb/Servers/Predict1/Predict1.html
Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program.
Proper citation: RNAstructure (RRID:SCR_017216) Copy
https://www.bmh.manchester.ac.uk/research/facilities/bioinformatics/
Core provides assistance in integrative analysis of genomic datasets to support faculty.
Proper citation: University of Manchester Bioinformatics Core Facility (RRID:SCR_017171) Copy
https://www.ie-freiburg.mpg.de/
Interdisciplinary research institute that conducts basic research in modern immunobiology, developmental biology and epigenetics.
Proper citation: Max Planck Institiute of Immunobiology and Epigenetics; Freiburg; Germany (RRID:SCR_017170) Copy
http://kim.bio.upenn.edu/software/pivot.shtml
Software R package for interactive analysis and visualization of transcriptomics data. Operating systems are macOS, Linux, Windows.
Proper citation: PIVOT software (RRID:SCR_017210) Copy
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