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http://acb.qfab.org/acb/glam2/
Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets.
Proper citation: Glam2 (RRID:SCR_016129) Copy
Software toolkit for biological sequence analysis and -presentation combined into a single binary. It is used for genome analysis, efficient processing of structured genome annotations and contains binaries for sequence and annotation handling, sequence compression, index structure generation and access, annotation visualization.
Proper citation: GenomeTools (RRID:SCR_016120) Copy
Software that employs machine learning techniques and high-performance computing for analyzing task-based fMRI datasets. It applies Feature Analysis, Hyperalignment, Multi-voxel Pattern Analysis (MVPA), Representational Similarity Analysis (RSA), and more.
Proper citation: Easy fMRI (RRID:SCR_016392) Copy
https://gemma.msl.ubc.ca/phenotypes.html
Database that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. Part of Gemma, a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data.
Proper citation: Phenocarta (RRID:SCR_016273) Copy
Web based software for analyzing genomic variants CNVs, SNVs, and Indels and phenotypes. It aims to represent the relationships between discovered variants and phenotypes.
Proper citation: AspireDB (RRID:SCR_016272) Copy
https://www.ncbi.nlm.nih.gov/pubmed/23489480
Software package for image analysis to determine the orientation of filamentous structures on digital images. Used as an image‐processing tool for analyzing cytoskeleton and cellulose fiber orientation in pant imagesk.
Proper citation: MicroFilament Analyzer (RRID:SCR_016411) Copy
http://www.nitrc.org/projects/gimme/
Software Matlab toolbox for directed functional connectivity analysis of fMRI BOLD signal from predefined regions of interest. It recovers true structure of connections and estimates weights attributed to each connection. Obtains patterns at group and individual levels.
Proper citation: GIMME (RRID:SCR_014115) 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://accelrys.com/products/collaborative-science/biovia-pipeline-pilot/
Software used to automate the process of accessing, analyzing and reporting scientific data. This software can be used by a person with little or no software development experience can create scientific protocols that can be executed through a variety of interfaces including: BIOVIA Web Port, other BIOVIA solutions such as BIOVIA Electronic Lab Notebook, Isentris, Chemical Registration and third-party applications such as Microsoft SharePoint. The protocols aggregate and provide immediate access to volumes of research data, they automate the scientific analysis of data and allow researchers to explore, visualize and report results.
Proper citation: Pipeline Pilot (RRID:SCR_014917) Copy
https://github.com/broadinstitute/pilon/
Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome.
Proper citation: Pilon (RRID:SCR_014731) 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
https://sanger-pathogens.github.io/Roary/
Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes.
Proper citation: Roary (RRID:SCR_018172) 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
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
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