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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://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
https://bioconductor.org/packages/release/bioc/html/scran.html
Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection.
Proper citation: scran (RRID:SCR_016944) Copy
http://bioconductor.org/packages/release/bioc/html/ConsensusClusterPlus.html
Software written in R for determining cluster count and membership by stability evidence in unsupervised analysis. Provides quantitative and visual stability evidence for estimating the number of unsupervised classes in a dataset with item tracking, item consensus and cluster consensus plots.
Proper citation: ConsensusClusterPlus (RRID:SCR_016954) Copy
https://github.com/maypoleflyn/BSATOS
Software tools for next generation sequencing based bulked segregation analysis for outbreeding species including fruit trees such as apple or cirtus. Used to improve gene mapping efficiency of next generation sequencing based segregant analysis in outbreeding species and realize rapid candidate gene mining based on multi-omics data.
Proper citation: Bulked segregation analysis tools for outbreeding species (RRID:SCR_017009) 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
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
Software R package of multivariate methods for the exploration and integration of biological datasets with a focus on variable selection. Used to analyse data from high throughput sequencing technologies and spectral imaging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: mixOmics (RRID:SCR_016889) 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
https://uk.mathworks.com/matlabcentral/fileexchange/8797-tools-for-nifti-and-analyze-image
Matlab based scripts for load, save, make, reslice, view and edit both Neuroimaging Informatics Technology Initiative (NIfTI) and ANALYZE data on any platform.
Proper citation: Tools for NIfTI and ANALYZE image (RRID:SCR_016895) Copy
https://github.com/SofieVG/FlowSOM
Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise.
Proper citation: FlowSOM (RRID:SCR_016899) Copy
https://github.com/gelles-brandeis/CoSMoS_Analysis
Software tools for analyzing co-localization single-molecule spectroscopy image data.
Proper citation: CoSMoS_Analysis (RRID:SCR_016896) Copy
https://github.com/ICB-DCM/PESTO
Software customizable toolbox for parameter estimation in MathWorks MATLAB. Offers scalable algorithms for optimization, uncertainty and identifiability analysis which do not depend on any problem-specific assumptions.
Proper citation: PESTO (RRID:SCR_016891) Copy
https://github.com/qiicr/dcmqi
Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer.
Proper citation: dcmqi (RRID:SCR_016933) Copy
Software tool for data analysis and exploration. Statistics software for Mac.
Proper citation: Wizard (RRID:SCR_016939) 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
https://www.networkanalyst.ca/
Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data.
Proper citation: NetworkAnalyst (RRID:SCR_016909) Copy
http://nrtdp.northwestern.edu/
Organization dedicated to analysis of protein molecules by mass spectrometry, with a focus on intact protein measurements. Biomedical projects originated from clinical and basic research programs that utilize both targeted and untargeted analyses. Used for the development of new technology, training and dissemination of proteomics methods to laboratories and scientists.
Proper citation: National Resource for Translational and Developmental Proteomics (RRID:SCR_016907) 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
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