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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.
https://github.com/open2c/pairtools
Software command line framework to process sequencing data from Hi-C experiment. Used to process pair end sequence alignments.
Proper citation: pairtools (RRID:SCR_023038) Copy
https://github.com/hartwigmedical/hmftools/blob/master/purple/README.md
Software tool as purity ploidy estimator for whole genome sequenced data. Used for copy number calling and determination of sample purity.
Proper citation: PURPLE (RRID:SCR_022999) Copy
Software to visualize and qualitatively analyze mass spectrometry data. Used to display chromatograms and spectra, detect and integrate chromatographic peaks, search mass spectral libraries, simulate mass spectra, subtract background spectra, apply scan filters, annotate plots with text and graphics, create and save layouts, view the status of various instrument parameters during data acquisition, and create a 2D or 3D representation of an analysis displaying the acquired mass/wavelength scans. Part of liquid chromatography mass spectrometry system.
Proper citation: FreeStyle 1.8 SP1 (RRID:SCR_022877) Copy
https://github.com/walaj/svaba
Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements.
Proper citation: SvABA (RRID:SCR_022998) Copy
http://cell-innovation.nig.ac.jp/maser/AllPipelines/P000001138_en.html
Software pipeline that visualizes mapping results (in BAM format) on Genome Explorer.
Proper citation: loadBAM2ge_db (RRID:SCR_015951) Copy
https://www.pinnaclet.com/sleepPRO.html
Software tool to reduce scoring time and simplify data analysis. Offers automated power analysis, semi-automated scoring methods, and advanced tabular and graphical analysis for investigating sleep data sets. Custom scoring and analysis are also available. Scoring sessions between two or more users can be compared. All EEG/EMG and video data sets recorded with Pinnacle software, as well as third party EDF files, can be imported.
Proper citation: Sirenia Sleep Pro (RRID:SCR_022918) Copy
Repository of metadata and data that describes and provides access to diverse data sets generated by Arctic and Antarctic researchers.Metadata records follow ISO 19115 and Federal Geographic Data Committee standard formats to provide exchange with other data centres.Records cover wide range of disciplines from natural sciences and policy, to health and social sciences. The PDC Geospatial Search tool is available to the public and researchers alike and allows searching data using mapping interface and other parameters.
Proper citation: Canadian Polar Data Network (RRID:SCR_023143) Copy
Provides open access to Climate and Earth System Data from scientists at the centre and their collaborators. Helps to make your data open, FAIR and visually appealing. Each dataset and source code in the Bolin Centre Database is assigned a unique DOI. This makes it easy to cite and find your data. If dataset has more than one version, each version will have its own DOI.
Proper citation: Bolin Centre Database (RRID:SCR_023142) Copy
https://www.genoscope.cns.fr/brassicanapus/
Web tool as Brassica napus genome browser.
Proper citation: CNS Genoscope (RRID:SCR_023020) Copy
https://github.com/c-zhou/yahs
Software command line tool for construction of chromosome scale scaffolds from Hi-C data. Scaffolding tool using Hi-C or Omni-C data. Used to scaffold contig level assemblies into chromosome scale scaffolded assemblies.
Proper citation: YaHS (RRID:SCR_022965) Copy
Astronomical data archive focused on optical, ultraviolet, and near infrared. Used for maximizing scientific accessibility and productivity of astronomical data. MAST hosts data from over dozen missions like Webb, Hubble, TESS, Kepler, and in the future Roman.
Proper citation: Barbara A. Mikulski Archive for Space Telescopes (RRID:SCR_023137) Copy
https://github.com/saeyslab/nichenetr
Software tool as R implementation of NicheNet method to predict active ligand-target links between interacting cells. NicheNet uses human or mouse gene expression data of interacting cells as input and combines this with prior model that integrates existing knowledge on ligand-to-target signaling paths. This allows to predict ligand-receptor interactions that might drive gene expression changes in cells of interest.
Proper citation: NicheNet (RRID:SCR_023158) Copy
http://www.vsh.com/products/mflt/index.asp
Modeling software for flow cytometry histograms. Models for cell-tracking dye studies and synchronized cell lines are built right into the software.
Proper citation: ModFit LT (RRID:SCR_016106) Copy
https://www.emkatech.com/product/iox2-software/
Software tool to acquire, analyze, view, and store physiological data generated during preclinical experiment. Has library of application specific analysis modules for real time signal processing.
Proper citation: IOX2 (RRID:SCR_022973) Copy
HTAN is National Cancer Institute funded Cancer Moonshot initiative to construct 3-dimensional atlases of dynamic cellular, morphological, and molecular features of human cancers as they evolve from precancerous lesions to advanced disease.Provides three dimensional atlases of cancer transitions for diverse set of tumor types. Efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at single point in time. Data portal for Human Tumor Atlas Network. Data available on HTAN Portal is open access. Certain data types with potential for re-identification are available in restricted access through dbGAP.
Proper citation: Human Tumor Atlas Network (RRID:SCR_023364) Copy
Software metadata ingestion platform that helps to improve quality of metadata. Station allows users to record meta-data according to minimum information standards thereby ensuring FAIR scientific data management from the start.
Proper citation: FAIR Data Station (RRID:SCR_023239) Copy
https://github.com/openMetadataInitiative/openMINDS_SANDS
One of the metadata models of openMINDS metadata framework. Composed of modular metadata schemas for spatial anchoring of neuroscience data structures, including brain atlas definitions.
Proper citation: openMINDS SANDS metadata model (RRID:SCR_023498) Copy
https://www.intelligent-imaging.com/slidebook.php
Digital microscopy software for research microscopy. It comes standard with drivers to control numerous instruments in and around the microscope. When online, data is acquired in a native-3D format over time, color and specimen locations in customizable experiment protocols. Data can be analyzed by a wide variety of tools for image processing including mathematical operations, statistics functions, analysis scripting and import to/export from MATLAB. Additional modules are available for special applications ranging from deconvolution to photomanipulation to multiphoton.
Proper citation: SlideBook (RRID:SCR_014423) Copy
https://cell-innovation.nig.ac.jp/maser/Tools/visualization_top_en.html
One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGffToGe_db for custom genome software loads GFF files of custom genomes to a database for Genome Explorer. It allows the user to browse the results through the GE.
Proper citation: loadGffToGe_db for custom genome (RRID:SCR_015997) Copy
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