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https://bitbucket.org/biobakery/biobakery/wiki/Home
Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: biobakery (RRID:SCR_016596) Copy
Software tool for microarray analysis designed for biologists . Used for identification of differential expression by providing interactive visualizations.
Proper citation: Transcriptome Analysis Console (RRID:SCR_016519) Copy
http://www.dhal.com/viewboxindex.htm
Software for cephalometric analysis. Customizable. Allows rendering, viewing and measuring of 3D data from CT scanners. Used in orthodontic departments for analysis of the dental and skeletal relationships of a human skull.
Proper citation: Viewbox4, Cephalometric software (RRID:SCR_016481) Copy
Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics.
Proper citation: PhenoMeNal (RRID:SCR_016605) Copy
https://niaid.github.io/spice/
Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically.
Proper citation: SPICE (RRID:SCR_016603) 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://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
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/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
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 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
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