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https://www.bioconductor.org/packages/release/bioc/html/ensembldb.html
Software R package to create and use Ensembl based annotation resources.
Proper citation: ensembldb (RRID:SCR_019103) Copy
https://gitlab.com/biomerieux-data-science/clustlasso
Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach.
Proper citation: clustLasso (RRID:SCR_018820) Copy
https://github.com/big-data-lab-team/spot
Open source software tool for file based localization of numerical perturbations in data analysis pipelines. Identifies components in pipeline, at resolution level of system process, that produce different results in different execution conditions.
Proper citation: Spot (RRID:SCR_018915) Copy
https://cran.r-project.org/web/packages/GALLO/vignettes/GALLO.html
Software R package developed for accurate annotation of genes and quantitative trait loci located in regions identified in common genomic analyses performed in livestock, such as Genome Wide Association Studies and transcriptomics using RNA-Sequencing. Allows graphical visualization of gene and QTL annotation results, data comparison among different grouping factors like methods, breeds, tissues, statistical models, studies and QTL enrichment in different livestock species including cattle, pigs, sheep, and chickens.
Proper citation: Genomic Annotation in Livestock for positional candidate LOci (RRID:SCR_019212) Copy
https://github.com/SMI/SmiServices
Software suite of tools for cataloguing and anonymising DICOM files, as used for Scottish Medical Imaging project. Software suite of microservices for loading, anonymising, linking and extracting large volumnes of dicom medical images to support medical research. Platform allows dicom tags extracted from clinical images to be loaded into MongoDB and relational database tables for purposes of generating anonymous linked research extracts including image anonymisation.
Proper citation: SMI Services (RRID:SCR_018881) Copy
Databases and portal to data and ordering mouse strains from MRC Harwell including mouse stocks in FESA (Frozen Embryo and Sperm Archive), mutants from the mutagenesis screen, the ENU DNA archive, standardized phenotyping procedures, imprinting genes and chromosome anomalies. The portal integrates curated information from the MRC Harwell stock resource, and other Harwell databases, with information from external data resources to provide added value information above and beyond what is available through other routes such as IMSR (International Mouse Stain Resource). MouseBook can be searched either using an intuitive Google-style free text search or using the Mammalian Phenotype Ontology (MP) tree structure. Text searches can be on gene, allele, strain identifier (e.g. MGI ID) or phenotype term and are assisted by automatic recognition of term types and autocompletion of gene and allele names covered by the database. Results are returned in a tabbed format providing categorized results identified from each of the catalogs in MouseBook. Individual results lines from each catalog include information on gene, allele, chromosomal location and phenotype and provide a simple click-through link to further information as well as ordering the strain. The infrastructure underlying MouseBook has been designed to be extensible, allowing additional data sources to be added enabling other sites to make their data directly available through MouseBook.
Proper citation: MouseBook (RRID:SCR_006358) Copy
The free Segway software package contains a novel method for analyzing multiple tracks of functional genomics data. The method uses a dynamic Bayesian network (DBN) model, which enables it to analyze the entire genome at 1-bp resolution even in the face of heterogeneous patterns of missing data. This method is the first application of DBN techniques to genome-scale data and the first genomic segmentation method designed for use with the maximum resolution data available from ChIP-seq experiments without downsampling. Segway uses the Graphical Models Toolkit (GMTK) for efficient DBN inference. The software has extensive documentation and was designed from the outset with external users in mind.
Proper citation: Segway - a way to segment the genome (RRID:SCR_004206) Copy
http://cudasw.sourceforge.net/
CUDASW++ is a bioinformatics software for Smith-Waterman protein database searches that takes advantage of the massively parallel CUDA architecture of NVIDIA Tesla GPUs to perform sequence searches 10x-50x faster than NCBI BLAST. In this algorithm, we deeply explore the SIMT (Single Instruction, Multiple Thread) and virtualized SIMD (Single Instruction, Multiple Data) abstractions to achieve fast speed. This algorithm has been fully tested on Tesla C1060, Tesla C2050, GeForce GTX 280 and GTX 295 graphics cards, and has been incorporated to NVIDIA Tesla Bio Workbench. * Operating System: Linux * Programming language: CUDA and C * Other requirements: CUDA SDK and Toolkits 2.0 or higher
Proper citation: CUDASW++ (RRID:SCR_008862) Copy
http://bioen-compbio.bioen.illinois.edu/FusionHunter/
Software for identifying fusion transcripts using paired-end RNA-seq.
Proper citation: FusionHunter (RRID:SCR_011895) Copy
https://cran.r-project.org/web/packages/ggplot2/index.html
Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.
Proper citation: ggplot2 (RRID:SCR_014601) Copy
http://dgrapov.github.io/MetaMapR/
An open-source software program for integrating enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate connected metabolic networks and display results using data visualization techniques.
Proper citation: MetaMapR (RRID:SCR_014685) Copy
:OsiriX is an image processing software dedicated to DICOM images (.dcm / .DCM extension) produced by medical equipment (MRI, CT, PET, PET-CT, ...) and confocal microscopy (LSM and BioRAD-PIC format). It can also read many other file formats: TIFF (8,16, 32 bits), JPEG, PDF, AVI, MPEG and Quicktime. It is fully compliant with the DICOM standard for image comunication and image file formats. OsiriX is able to receive images transferred by DICOM communication protocol from any PACS or medical imaging modality (STORE SCP - Service Class Provider, STORE SCU - Service Class User, and Query/Retrieve) . OsiriX has been specifically designed for navigation and visualization of multimodality and multidimensional images: 2D Viewer, 3D Viewer, 4D Viewer (3D series with temporal dimension, for example: Cardiac-CT) and 5D Viewer (3D series with temporal and functional dimensions, for example: Cardiac-PET-CT). The 3D Viewer offers all modern rendering modes: Multiplanar reconstruction (MPR), Surface Rendering, Volume Rendering and Maximum Intensity Projection (MIP). All these modes support 4D data and are able to produce image fusion between two different series (for example: PET-CT). Osirix is at the same time a DICOM PACS workstation for medical imaging and an image processing software for medical research (radiology and nuclear imaging), functional imaging, 3D imaging, confocal microscopy and molecular imaging. :
Proper citation: OsiriX Medical Imaging Software (RRID:SCR_013618) Copy
https://knights-lab.github.io/MLRepo/
Machine learning repository for microbiome datasets.
Proper citation: ML Repo (RRID:SCR_017079) Copy
https://amp.pharm.mssm.edu/geneshot/
Software tool as search engine for ranking genes from arbitrary text queries. Enables to enter arbitrary search terms, to receive ranked lists of genes relevant to search terms. Returned ranked gene lists contain genes that were previously published in association with search terms, as well as genes predicted to be associated with terms based on data integration from multiple sources. Search results are presented with interactive visualizations.
Proper citation: Geneshot (RRID:SCR_017582) Copy
http://www.cbs.dtu.dk/services/NetMHCpan/
Web server for quantitative prediction of peptide binding to any MHC molecule of known sequence using artificial neural networks. Characterizes binding specificity of given major histocompatibility complex molecule and predicts peptide length profile and peptide binding affinity. NetMHCpan 3.0 is improved prediction of binding to MHC class I molecules integrating information from multiple receptor and peptide length data sets. NetMHCpan 4.0 is trained on naturally eluted ligands and on peptide binding affinity data. NetMHCpan-4.1 server predicts binding of peptides to any MHC molecule of known sequence using artificial neural networks (ANNs).
Proper citation: NetMHCpan Server (RRID:SCR_018182) Copy
https://github.com/TomSexton00/4See
Software tool to visualize 4C data.
Proper citation: 4See (RRID:SCR_018014) Copy
https://github.com/hangyabalazs/opeth
Software tool to enable flexible online visualization of action potential alignment to external events. Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them.
Proper citation: Online Peri-Event Time Histogram for Open Ephys (RRID:SCR_018022) Copy
http://wpicr.wpic.pitt.edu/WPICCompGen/bars.htm
Software application that is a statistical method that bridges the gap between single-locus and haplotype-based tests of association. It is based on the non-parametric regression techniques embodied by Bayesian Adaptive Regression Splines. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: BARS (RRID:SCR_009123) Copy
Software for syntax highlighting for computational biology.
Proper citation: bioSyntax (RRID:SCR_016207) Copy
https://code.google.com/p/ms-lims/
Software that provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data.
Proper citation: ms lims (RRID:SCR_002974) Copy
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