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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.
Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise.
Proper citation: Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS (RRID:SCR_016657) Copy
https://visrsoftware.github.io/
Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses.
Proper citation: VisR (RRID:SCR_016658) Copy
https://software.broadinstitute.org/gatk/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer.
Proper citation: IndelGenotyper (RRID:SCR_016663) Copy
http://www.cbs.dtu.dk/biotools/sequenza/
Software package for copy number estimation from tumor genome sequencing data.Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.
Proper citation: Sequenza (RRID:SCR_016662) Copy
https://www.mbfbioscience.com/neurolucida360
Software for automatic neuron 3D reconstruction and analysis. Used by neuroscientists to reconstruct intricate neuronal structures that range in scale from complex, multicellular networks of neurons to sub-cellular dendritic spines and putative synapses.
Proper citation: Neurolucida 360 (RRID:SCR_016788) Copy
Web tool to search multiple public variant databases simultaneously and provide a unified interface to facilitate the search process. Used for integration of human and model organism genetic resources to facilitate functional annotation of the human genome. Used for analysis of human genes and variants by cross-disciplinary integration of records available in public databases to facilitate clinical diagnosis and basic research.
Proper citation: MARRVEL (RRID:SCR_016871) Copy
https://github.com/Crop-Phenomics-Group/CropSight
Software tool which is a PHP and SQL based server platform. Provides automated data collation, storage, and information management through distributed IoT sensors and phenotyping workstations. It provides a two-component solution to monitor biological experiments through networked sensing devices, with interfaces specifically designed for distributed plant phenotyping and centralized data management.
Proper citation: CropSight (RRID:SCR_016870) Copy
https://github.com/PathwayAnalysisPlatform/PathwayMatcher
Software tool for multi omics pathway mapping and proteoform network generation. Open source software writen in Java to search for pathways related to a list of proteins in Reactome.
Proper citation: PathwayMatcher (RRID:SCR_016759) Copy
https://github.com/reinkk/Growth-Profiling-Toolbox
Software package as a growth curve automatic processing pipeline in Matlab.
Proper citation: Growth Profiling Toolbox (RRID:SCR_016878) Copy
https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html
Web portal for global query cross database search and retrieval system that provides access to all databases simultaneously with a single query string and user interface. Retrieves nucleotide and protein sequence data, gene centered and genomic mapping information, 3D structures, and references. Covers databases including protein sequence data from PIR-International, PRF, Swiss-Prot, and PDB and nucleotide sequence data from GenBank that includes information from EMBL and DDBJ.
Proper citation: Entrez (RRID:SCR_016640) Copy
https://github.com/HussainiLab/hfoGUI
Graphical user interface to visualize EEG data. The applications can vary from scoring High Frequency Oscillations, to observing Theta and Gamma Synchrony.
Proper citation: hfoGUI (RRID:SCR_016726) Copy
https://cran.r-project.org/web/packages/RColorBrewer/index.html
Software tool to provide color schemes for maps and other graphics. R package to create colorful graphs with pre-made color palettes that visualize data.
Proper citation: RColorBrewer (RRID:SCR_016697) Copy
http://ec2-52-91-98-53.compute-1.amazonaws.com/run/
Web based platform that integrates several bioinformatics tools for screening and annotation of cDNA construct sequences. Translates the nucleotide sequence of the construct into an amino acid sequence, aligns the predicted sequence to a reference database of protein sequences and identifies the best protein and isoform match, annotates any variants present in the construct, and incorporates disease-associated mutations and transcriptomic data.
Proper citation: Clonotator (RRID:SCR_016730) Copy
http://www.thomaskoenig.ch/index.php/software/ragu
Software tool for the analysis of EEG and MEG event-related scalp field data using global randomization statistics.
Proper citation: Ragu (RRID:SCR_016851) Copy
https://sites.google.com/view/diegoalvarezestevez/projects/polyman
Software tool as an European Data Format EDF/EDF+ viewer and manual sleep scoring program. Used in EEG and Sleep investigations, but can be used for almost any (also non-medical) sequential time series and event lists.
Proper citation: Polyman (RRID:SCR_016850) Copy
http://emg.nysbc.org/redmine/projects/leginon/wiki/Leginon_Homepage
System designed for automated collection of images from a transmission electron microscope.
Proper citation: Leginon (RRID:SCR_016731) Copy
Software framework for image processing to obtain 3D models of macromolecular complexes using Electron Microscopy. Open-source project for integration, reproducibility and validation in 3D electron microscopy. It integrates several software packages to execute workflows combining different software tools, while taking care of formats and conversions. Electron Microscopy (3DEM). waiting for pdf from Joe
Proper citation: SCIPION (RRID:SCR_016738) Copy
http://metascape.org/gp/index.html#/main/step1
Web service to analyze gene or protein lists. Provides automated meta analysis tools to understand pathways within a group of orthogonal target-discovery studies.
Proper citation: Metascape (RRID:SCR_016620) Copy
https://github.com/yarden/MISO/blob/fastmiso/docs/source/sashimi.rst
Software tool for quantitative visualization of aligned RNA-Seq reads that enables quantitative comparison of exon usage across samples or experimental conditions.
Proper citation: Sashimiplot (RRID:SCR_016861) Copy
https://github.com/CPernet/spmup/
Software Project Management (SPM) tools which contain a collection of functions that can be used at different stage of a standard massive univariate fMRI data analysis. Used to improve mass univariate analysis.
Proper citation: SPM U+ (RRID:SCR_016743) Copy
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