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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 package to detect and quantify local splicing variations (LSV) from RNA-Seq data. Used to automatically detect and downweight outliers in RNA-Seq datasets with replicates for differential splicing (SD) analysis.
Proper citation: MAJIQ (RRID:SCR_016706) Copy
https://github.com/fyz11/MOSES
Computational Python library for the motion analysis of biological single-cell and collective motion for high content screens. Framework to quantify and discover cellular motion phenotypes.
Proper citation: Motion Sensing Superpixels (MOSES) (RRID:SCR_016839) Copy
https://github.com/xia-lab/MetaboAnalystR
Software R package for comprehensive analysis of metabolomics data. Contains the R functions and libraries underlying MetaboAnalyst web server, including functions for metabolomic data analysis, visualization, and functional interpretation.
Proper citation: MetaboAnalystR (RRID:SCR_016723) Copy
Software package for image acquisition, analysis, display, and archiving. Used to quantify the autoradiography data from Cyclone apparatus from Perkin Elmer.
Proper citation: OptiQuant Software (RRID:SCR_016769) Copy
Web platform for bio image analysis. Used to share knowledge between the different communities, to help biologists to find any tool or workflow available for a particular image analysis problem and to find the adequate image processing wording, to help software and algorithm developers to find missing tools (or components), and to help bioimage analyst to identify and edit workflows.
Proper citation: BISE (RRID:SCR_016774) Copy
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
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
Software packages for quantitative cell analysis. Used in image cytometry, quantitative cell analysis or automated cell analysis in biological research and drug discovery.
Proper citation: HCS Studio Cell Analysis software (RRID:SCR_016787) 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://software.broadinstitute.org/software/discovar/blog/
Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes.
Proper citation: Discovar assembler (RRID:SCR_016755) 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
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://joinsolver.niaid.nih.gov
Software tool to analyze human immunoglobulin V(D)J recombination and performing Ig nucleotide and amino acid alignment, as well as extensive mutation and Complementarity Determining Region 3 (CDR3H) analysis.
Proper citation: JOINSOLVER (RRID:SCR_016619) Copy
https://www.niaid.nih.gov/research/simmune-project
Software package to define the interactions between individual molecules in a large network or the behaviors of cells in response to external signals. It consists of three components: Modeler, Cell Designer and Simulator.
Proper citation: Simmune (RRID:SCR_016618) 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
Software Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
Proper citation: NetworkX (RRID:SCR_016864) Copy
https://bioconductor.org/packages/release/bioc/html/riboSeqR.html
Software tool for analysis of sequencing data from ribosome profiling experiments. Used for plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.
Proper citation: riboSeqR (RRID:SCR_016947) Copy
https://bioconductor.org/packages/release/bioc/html/Rsubread.html
Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers.
Proper citation: Rsubread (RRID:SCR_016945) Copy
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