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https://mskkp.org/

Portal enables browsing, searching, and analysis of human genetic and genomic information linked to musculoskeletal traits and diseases, while protecting the integrity and confidentiality of underlying data.

Proper citation: Musculoskeletal Knowledge Portal (RRID:SCR_023171) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.thermofisher.com/de/de/home/technical-resources/technical-reference-library/mass-spectrometry-support-center/liquid-chromatography-mass-spectrometry-software-support/freestyle-software-support/freestyle-software-support-getting-started.html

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.genoscope.cns.fr/brassicanapus/

Web tool as Brassica napus genome browser.

Proper citation: CNS Genoscope (RRID:SCR_023020) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.abbiotec.com/

An Antibody supplier

Proper citation: Abbiotec (RRID:SCR_013596) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://humantumoratlas.org

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   

•   Source: SciCrunch Registry

http://fairbydesign.nl

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://naturalscenesdataset.org/

Portal for large scale fMRI dataset conducted at ultra high field strength at Center of Magnetic Resonance Research at University of Minnesota. Dataset consists of whole brain, high resolution fMRI measurements of healthy adult subjects while they viewed thousands of color natural scenes over course of scan sessions. While viewing these images, subjects were engaged in continuous recognition task in which they reported whether they had seen each given image at any point in experiment. These data constitute massive benchmark dataset for computational models of visual representation and cognition, and can support wide range of scientific inquiry.

Proper citation: Natural Scenes Dataset (RRID:SCR_023648) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://github.com/VH-Lab/vhlab-TwoPhoton-matlab

Software VH Lab tools for analysis of calcium imaging data. Allows selection of ROIs and extraction of time series data from raster-scanned, line-scanned, or CCD images, written in Matlab.

Proper citation: vhlab-TwoPhoton-matlab (RRID:SCR_023369) Copy   

•   Source: SciCrunch Registry

https://bdcw.org/MetGENE/index.php

Web tool identifies associations between genes and metabolites that are biosynthesized, metabolized, or transported by proteins coded by genes. Gene centric metabolomics information retrieval tool. Knowledge based, gene centric data aggregator that hierarchically retrieves information about genes, their related pathways, reactions,metabolites, and metabolomic studies from standard data repositories under one dashboard to enable ease of access through centralization of relevant information. Information can be contextualized by filtering along species, anatomy tissue and disease or phenotype.

Proper citation: MetGENE (RRID:SCR_023402) Copy   

•   Source: SciCrunch Registry

http://www.partec.de

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1,2023. Partec uses FloMax software on most cytometers, which produces FCS 3.0 compliant files. FloMax rescales the fluorescent data on the acquisition display without changing the stored values.

Proper citation: partec flomax (RRID:SCR_014026) Copy   

•   Source: SciCrunch Registry