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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
Web application and database designed for sharing, visualizing, and analyzing protein cross-linking mass spectrometry data with emphasis on structural analysis and quality control. Includes public and private data sharing capabilities, project based interface designed to ensure security and facilitate collaboration among multiple researchers. Used for private collaboration and public data dissemination.
Proper citation: Protein Cross-Linking Database (RRID:SCR_021027) Copy
Open source software analysis and visualization platform for microbial omics including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in integrated fashion through extensive interactive visualization capabilities.
Proper citation: Anvi'o (RRID:SCR_021802) Copy
https://ccb.jhu.edu/software/stringtie/
Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ .
Proper citation: StringTie (RRID:SCR_016323) Copy
http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/MrDiffusion
Software package for diffusion imaging analysis and visualization. Module of Vistasoft for processing diffusion weighted data and measuring and visualizing fractional anisotropy, mean diffusivity, axial and radial diffusivity, RGB fiber direction maps and analysis of MRI data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MrDiffusion (RRID:SCR_016567) Copy
Interactive scientific development environment package for Python. Used for editing, analysis, debugging, and profiling functionality of comprehensive development tool with data exploration, interactive execution, deep inspection, and visualization.
Proper citation: Spyder (RRID:SCR_017585) Copy
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.
Proper citation: DESeq2 (RRID:SCR_015687) Copy
http://ikrsrv1.medma.uni-heidelberg.de/redmine/projects/ummperfusion
Analysis software for dynamic contrast enhanced magnetic resonance images with implementation of a pixel-by-pixel deconvolution approach. It quantifies T1-weighted contrast-enhanced dynamic MR imaging (DCE-MRI) perfusion data as an OsiriX plug-in.
Proper citation: UMMPerfusion (RRID:SCR_015970) Copy
Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud).
Proper citation: FreeContact (RRID:SCR_016113) Copy
http://www.uimcimes.es/contenidos/golink?p=1
Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences.
Proper citation: QModeling (RRID:SCR_016358) Copy
http://hms-dbmi.github.io/scde/index.html
Software package that implements a set of statistical methods for analyzing single-cell RNA-seq data, including differential expression analysis (Kharchenko et al.) and pathway and geneset overdispersion analysis (Fan et al.)
Proper citation: SCDE (RRID:SCR_015952) Copy
https://cran.r-project.org/web/packages/geomorph/index.html
Software package for performing all stages of geometric morphometric shape analysis of landmark points and curves in 2-and-3-dimensions as well as 3D surfaces in the R statistical computing environment.
Proper citation: geomorph (RRID:SCR_016482) Copy
Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data.
Proper citation: Brain Imaging Analysis Kit (RRID:SCR_014824) Copy
http://bioinformatics.uni-muenster.de/tools/nanopipe2
Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms.
Proper citation: NanoPipe (RRID:SCR_016852) Copy
https://www.uke.de/english/research/core-facilities/bioinformatics-core-en.html
Core provides bioinformatics services for researchers at University Medical Center Hamburg Eppendorf and related institutions. Focusing on high throughput sequencing data. Services include data analysis, consulting, software development, and bioinformatical training.
Proper citation: University Medical Center Hamburg-Eppendorf Bioinformatics Core Facility (RRID:SCR_017144) Copy
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