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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.
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
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
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
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
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://github.com/tobiasrausch/alfred
Web application as interactive multi-sample BAM alignment statistics, feature counting and feature annotation for long- and short-read sequencingas.
Proper citation: Alfred (RRID:SCR_023354) 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
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
Comparative database with clinical and resource utilization data for inpatient, ambulatory surgery, emergency department and observation unit encounters for more than 49 children's hospitals.
Proper citation: Children's Hospital Association Pediatric Health Information System (RRID:SCR_023168) Copy
Bibliography covering all publications related to the fast-growing field of biomedical literature and text mining. This forum for collecting, compiling and sharing is a one-stop resource, letting researchers find out who-does-what in the area and where it is published, bridging across the many discipline-specific venues in which biomedical text-mining papers are published. If you know of a relevant paper that is missing from BLIMP, or have an accepted-for-publication paper, PhD/MSc thesis or a technical report, that you believe is relevant to biomedical text mining, fill in the submission form. The fast-growing field of biomedical literature mining is highly-interdisciplinary. Publications appear in forums ranging from the SIGIR conferences (the ACM Special Interest group on Information Retrieval) to journals such as Nature and Science, with the whole range of bioinformatics forums in-between. To substantially contribute, one must know what was/is being done in this diverse area, and place the work in context - both biologically and computationally. Instead of starting a journal fully dedicated to biomedical literature mining, thus creating yet another publication venue, this site offers an alternative: It holds in one place a compilation of references to relevant papers that have been published or accepted for publication.
Proper citation: BLIMP: Biomedical LIterature Mining Publications (RRID:SCR_007112) 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
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