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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/hetio/hetmatpy
Software Python package for matrix storage and operations on hetnets. Enables identifying relevant network connections between set of query nodes.
Proper citation: HetMatPy (RRID:SCR_023409) Copy
https://pillow.readthedocs.io/en/stable/
Software Python Imaging Library adds image processing capabilities to your Python interpreter. This library provides extensive file format support, efficient internal representation, and image processing capabilities. Core image library is designed for fast access to data stored in few basic pixel formats. It should provide solid foundation for general image processing tool.
Proper citation: pillow (RRID:SCR_023337) Copy
Open access integrated research platform, which links scientists, shared data, and analysis tools to accelerate Alzheimer’s disease research, disease preventions, treatments and cure. Unites diverse and geographically distributed network of data partners to foster cohort discovery, collaboration and sharing. Researchers can discover clinical, genetic, imaging and other data collected across many independent studies.
Proper citation: Global Alzheimers Association Interaction Network (RRID:SCR_023699) Copy
https://bioconductor.org/packages/release/bioc/html/mia.html
Software R package with several tools for microbiome data analysis.
Proper citation: mia (RRID:SCR_023619) Copy
https://www.cancergenomeinterpreter.org/home
Platform that systematizes interpretation of cancer genomes and makes it automatic. Web tool to annotate genomic alterations and interpret their possible role in tumorigenesis and in response to anti cancer therapies. Used to support identification of tumor alterations that drive disease and/or which may be therapeutically actionable. Analyses mutations including single nucleotide changes and small insertions/deletions, copy number alterations including gene amplifications and deletions and translocations.
Proper citation: Cancer Genome Interpreter (RRID:SCR_023752) Copy
https://www.viewpoint.fr/product/zebrafish/cardiology/microzebralab
Software tool to extract cardiovascular parameters from transmitted light videos of zebrafish embryos or larvae. Used to investigate live and in non-invasive way scope of zebrafish larvae physiological parameters. Measures heartbeat and blood flow.
Proper citation: ViewPoint MicroZebraLab (RRID:SCR_023750) Copy
https://awi.cuhk.edu.cn/KinasePhos/download.html
Software tool for redesign and expansion of prediction on kinase specific phosphorylation sites. Machine learning based kinase specific phosphorylation site prediction tool.
Proper citation: KinasePhos 3.0 (RRID:SCR_023595) Copy
https://blobtoolkit.genomehubs.org/blobtools2/
Software suite for identifying and isolating non-target data in draft and publicly available genome assemblies. Used to process assembly, read and analysis files for fully reproducible interactive exploration in browser-based Viewer. Used for interactive quality assessment of genome assemblies .BlobTools2 is reimplementation of BlobTools, written in Python 3 with fully modular design to make creating new datasets and adding additional analysis types easier.
Proper citation: BlobTools2 (RRID:SCR_023351) Copy
https://github.com/citiususc/BigSeqKit
Software parallel Big Data toolkit to process FASTA and FASTQ files at scale. Used to manipulate FASTA/Q files at scale with speed and scalability at its core.
Proper citation: BigSeqKit (RRID:SCR_023592) Copy
Resource enables integrative exploration of genetic and epigenetic basis of development of Type 2 Diabetes, together with other associated functional, molecular and clinical data, centered in biology and role of pancreatic beta cells.The gene expression regulatory variation landscape of human pancreatic islets.
Proper citation: TIGER Data Portal (RRID:SCR_023626) Copy
https://www.zeiss.com/microscopy/en/products/software/zeiss-zen-lite.html
Software tool for basic image acquisition and analysis. Zeiss ZEN microscopy software to control of axiocam microscope cameras, image transformation and measurements, image processing, image alignment for correlative microscopy, various visualization options.
Proper citation: Zeiss Zen Lite (RRID:SCR_023747) Copy
https://rth.dk/resources/risearch/
Software tool for prediction of RNA–RNA, RNA–DNA, and DNA–DNA interactions. Both RIsearch1 and RIsearch2 enable quick localisation of potential near complementary interactions between given query and target sequences. RIsearch1 performs computation with whole sequences. RIsearch2 focuses on perfect complementary seed regions and extends them on both ends. User defined seed and extension constraints makes RIsearch2 applicable to all kinds of interaction predictions (e.g., siRNA and Cas9–gRNA off-target predictions).
Proper citation: RIsearch (RRID:SCR_023503) Copy
Web service to predict involvement of upstream cell signaling pathways, given signature of differentially expressed genes. Used to linking expression signatures to upstream cell signaling networks.
Proper citation: X2K Web (RRID:SCR_023624) Copy
https://upsetplot.readthedocs.io/en/stable/
Software Python implementation of UpSet plots to visualize set overlaps.
Proper citation: UpSetPlot (RRID:SCR_023225) Copy
Platform that facilitates data driven hypothesis generation for diabetes and related metabolic disorder research community. Curated transcriptomics datasets from various Type 2 Diabetes studies are made available for download, visualization, and enrichment analysis.
Proper citation: Diabetes Data and Hypothesis Hub (RRID:SCR_023629) Copy
Republic of Korea e-Government platform for major domestic, international and North Korean statistics. Web service provides official statistics produced by statistical agencies covering more than 500 subject matters as well as the latest data on international finance and economy from international organizations i.e. IMF, World Bank, OECD.
Proper citation: Korea Statistical Information Service (RRID:SCR_023565) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 1, 2023. Software designed to take single or multi-wavelength intracellular ion measurements an provide simultaneous display of the raw data, ratio image, graphs of intensities, ratios, ion concentrations, and a non-ratiometric image for microscope techniques such as a brightfield or phase-contrast image. Two different ratiometric indicators can be imaged and measured simultaneously to provide greater insight to ion exchange and intracellular function regardless of dye loading concentrations, conditions, or emission intensities.
Proper citation: MetaFluor Fluorescence Ratio Imaging Software (RRID:SCR_014331) Copy
https://github.com/lucadellasantina/ObjectFinder
Software image analysis package for 3D object recognition in volumetric images developed for neuroscience research purposes. MATLAB application to recognize small structures in large volumetric image, plot their statistics and perform quantitative analysis such as nearest neighbor and colocalization analysis. Used to detect fluorescently labeled synapses in neuronal image stacks acquired using confocal or super resolution microscopes.
Proper citation: ObjectFinder (RRID:SCR_023319) Copy
https://neuromorpho.org/xyz2swc/ui/
Web service that converts all 30 reconstruction formats (and 65 variations) described in scientific literature into SWC standard. Service is available open-source through user-friendly browser interface and Application Programming Interface.
Proper citation: xyz2swc (RRID:SCR_023317) Copy
https://github.com/PedroBarbosa/VETA
Software tool that analyses performance of several variant prediction methods at different levels. Used to benchmark variant effect predictors from VCF files.
Proper citation: Variant Prediction Tools Evaluation (RRID:SCR_023314) Copy
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