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https://www.leica-microsystems.com/products/microscope-software/details/product/leica-las-x-ls/
Software for image capture, processing and analysis with Leica fluorescence and confocal microscopes.
Proper citation: Leica Application Suite X (RRID:SCR_013673) Copy
https://www.thermofisher.com/order/catalog/product/00-0210
Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis.
Proper citation: Thermo Fisher: GeneChip� Scanner 3000 7G (RRID:SCR_016522) Copy
Commercially provides services and products for research in the fields of molecular biology, diagnostics, enzymes and proteins.
Proper citation: NZYTech (RRID:SCR_016772) Copy
https://bionanogenomics.com/wp-content/uploads/2017/01/30047-Irys-User-Guide.pdf
System by BioNano Genomics ( formerly BioNanomatrix) which provides optical next generation mapping (NGM). Used for sequence assembly and structural variation analysis. Provides Scaffold Bionano genome mapping data with sequencing data to improve assembly contiguity, reduce sequencing coverage needed, and automatically correct errors in sequencing based assemblies.
Proper citation: BioNano: Irys system (RRID:SCR_016754) Copy
https://www.scanco.ch/microct100.html
Micro Computed Tomography 100 scanner for 3D imaging of specimens in vitro supplied with software for scanning, 3D analysis, visualization, image management and data import and export by SCANCO Medical AG.
Proper citation: Scanco: Medical microCT 100 system (RRID:SCR_017119) 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
Automatic Methane Potential Test System (AMPTS) II is analytical tool for conducting various anaerobic batch fermentation tests. This includes performing, with up to 15 test vials, biochemical methane potential (BMP) tests, anaerobic biodegradability studies, specific methanogenic activity (SMA) assays, as well as conducting residual gas potential (RGP) analyses on digested slurry.
Proper citation: BPC Instruments: Biomethane Potential Test (RRID:SCR_017319) Copy
Developer of medical software to offer image analysis technologies. Company in Denmark that provides medical image processing software to get quantifiable and accurate insight into brain.
Proper citation: Brainreader (RRID:SCR_017308) Copy
https://www.mangold-international.com/en/products/software/behavior-research-with-mangold-interact
Software platform for synchronized viewing and analysis of video footage and audio files in observational research by Mangold International GmbH. Qualitative and quantitative video coding software.
Proper citation: Interact (RRID:SCR_019254) Copy
https://www.labx.com/item/molecular-devices-molecular-dynamics-storm-860-molecular/3896212
Multifunction phosphoimager fluorimager laser scanner that collects fluorescent or storage phosphor images from gels, membranes and phosphor screens. It is equipped with blue (450 nm) and red (635 nm) lasers, can scan at resolutions down to 50 microns. It is able to quantify radioactive gels for commonly used isotopes such as 32P, 33P, 125I, 35S, and 14C. There are three detection modes: phosphor screen mode, red/blue fluorescence, chemifluorescence.
Proper citation: Molecular Devices: Molecular Dynamics Storm 860 Molecular Imager (RRID:SCR_018032) Copy
https://www.rcon-ndt.com/wp-content/uploads/Nanotom.pdf
System for scientific and industrial nanofocus computed tomography nanoCT and 3D metrology. Realizes unique spatial and contrast resolution on wide sample and application range. Used in material science, precision injection moulding, micromechanics, electronics geology and biology. Used in 3D CT applications. Allows many analysis, e.g. non-destructive visualization of slices, arbitrary sectional views, or automatic pore analysis.
Proper citation: GE: Phoenix Nanotom S (RRID:SCR_017995) Copy
A genome browser specialized in next-generation sequencing data.
Proper citation: GenomeJack (RRID:SCR_012026) Copy
Specializes in sequence and array-based SNP and copy number analysis, genetic association software, and analytic services. Their technologies empower scientists to determine the genetic causes of disease, transform drug discovery, develop genetic diagnostics, and advance the quest for personalized medicine.
Proper citation: Golden Helix Incorporated (RRID:SCR_012191) Copy
A curated database that provides comprehensive integrated biological information for Saccharomyces cerevisiae along with search and analysis tools to explore these data. SGD allows researchers to discover functional relationships between sequence and gene products in fungi and higher organisms. The SGD also maintains the S. cerevisiae Gene Name Registry, a complete list of all gene names used in S. cerevisiae which includes a set of general guidelines to gene naming. Protein Page provides basic protein information calculated from the predicted sequence and contains links to a variety of secondary structure and tertiary structure resources. Yeast Biochemical Pathways allows users to view and search for biochemical reactions and pathways that occur in S. cerevisiae as well as map expression data onto the biochemical pathways. Literature citations are provided where available.
Proper citation: SGD (RRID:SCR_004694) Copy
http://www.sbpdiscovery.org/technology/sr/Pages/LaJolla_StemCells.aspx
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. The former functions of this facility are split into two separate operations. The first is the generation and characterization of induced Pluripotent Stem Cells (iPSCs) is now being performed on a collaborative basis for both internal and external investigators with the Snyder lab. The second is a shared laboratory dedicated to the culture and analysis of stem cells that is available to SBP investigators.
Proper citation: Sanford Burnham Prebys Medical Discovery Institute Stem Cell Core (RRID:SCR_014856) Copy
https://w3.psychology.su.se/sleipner/
Software package as collection of modules implementing methods of analysis that form self-contained and empirically grounded toolbox for handling longitudinal data within person oriented paradigm.
Proper citation: sleipner (RRID:SCR_018143) Copy
https://CRAN.R-project.org/package=meta
Software general R package providing standard methods for meta analysis.
Proper citation: meta (RRID:SCR_019055) Copy
https://github.com/sqjin/CellChat
Software R toolkit for inference, visualization and analysis of cell-cell communication from single cell data.Quantitatively infers and analyzes intercellular communication networks from single-cell RNA-sequencing data. Predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Classifies signaling pathways and delineates conserved and context specific pathways across different datasets.
Proper citation: CellChat (RRID:SCR_021946) Copy
http://www.bcgsc.ca/platform/bioinfo/software/alea
A computational software toolbox for allele-specific (AS) epigenomics analysis. It incorporates allelic variation data within existing resources, allowing for the identification of significant associations between epigenetic modifications and specific allelic variants in human and mouse cells. It provides a customizable pipeline of command line tools for AS analysis of next-generation sequencing data (ChIP-seq, RNA-seq, etc.) that takes the raw sequencing data and produces separate allelic tracks ready to be viewed on genome browsers. ALEA takes advantage of the available genomic resources for human (The 1000 Genomes Project Consortium) and mouse (The Mouse Genome Project) to reconstruct diploid in-silico genomes for human or hybrid mice under study. Then, for each accompanying ChIP-seq or RNA-seq dataset, it generates two Wiggle track format (WIG) files from short reads aligned differentially to each haplotype.
Proper citation: ALEA (RRID:SCR_006417) Copy
http://www.cgat.org/~andreas/documentation/cgat/cgat.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 3, 2023. A collection of tools for the computational genomicist written in the python language to assist in the analysis of genome scale data from a range of standard file formats. The toolkit enables filtering, comparison, conversion, summarization and annotation of genomic intervals, gene sets and sequences. The tools can both be run from the Unix command line and installed into visual workflow builders, such as Galaxy. Please note that the tools are part of a larger code base also including genomics and NGS pipelines. Everyone who uses parts of the CGAT code collection is encouraged to contribute. Contributions can take many forms: bugreports, bugfixes, new scripts and pipelines, documentation, tests, etc. All contributions are welcome.
Proper citation: Computational Genomics Analysis Tools (RRID:SCR_006390) Copy
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