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https://github.com/jbelyeu/SV-plaudit
Software for rapidly curating structural variant (SVs) predictions. SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis.
Proper citation: SV-plaudit (RRID:SCR_016285) Copy
Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.
Proper citation: HyPhy (RRID:SCR_016162) Copy
https://sites.google.com/site/sigenproject/
Software to extract and trace neuronal structure from confocal laser scanning microscope images. It performs the automatic reconstruction of neurons for image stacks and can generate compartmental models of neurons as swc file format data.
Proper citation: SIGEN (RRID:SCR_016284) Copy
http://abacus.gene.ucl.ac.uk/software/indelible/
Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time.
Proper citation: Indelible (RRID:SCR_016163) Copy
https://github.com/sdparekh/zUMIs
Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information.
Proper citation: zUMIs (RRID:SCR_016139) Copy
https://www.microsoft.com/en-gb/
Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data.
Proper citation: Microsoft Excel (RRID:SCR_016137) Copy
https://sanger-pathogens.github.io/gubbins/
Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Gubbins (RRID:SCR_016131) Copy
http://www.medibeacon.com/preclinical/
Software used to analyze glomerular filtration rate (GFR) measurement from MediBeacon GFR monitor. It is used with the Transdermal Continuous Renal Function Monitor.
Proper citation: MediBeacon Studio Software (RRID:SCR_016252) Copy
Text-mining software that reviews methods sections of scientific articles. It provides a numerical score to represent the "reproducibility" of the article's research.
Proper citation: SciScore (RRID:SCR_016251) Copy
https://bitbucket.org/nsegata/graphlan/wiki/Home
Software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. Used for concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation as a high-resolution microbial tree of life with taxonomic annotations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: GraPhlAn (RRID:SCR_016130) Copy
Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence.
Proper citation: CycIF.org (RRID:SCR_016267) Copy
http://bioplex.hms.harvard.edu/
Database of cell lines with each expressing a tagged version of a protein from the ORFeome collection. The overarching project goal is to determine protein interactions for every member of the collection.
Proper citation: BioPlex (RRID:SCR_016144) Copy
Software that archives evidence collected from different sources, then analyzes and presents these data. Its data come from manually curated protein-protein interaction databases that have adhered to the IMEx consortium.
Proper citation: mentha (RRID:SCR_016148) Copy
Develops information technologies that make authoring complete metadata more manageable. Its products aim to facilitate using the metadata in further research.Center to improve metadata and its use throughout biomedical sciences. Develops information technologies that make authoring complete metadata more manageable through better interfaces, terminology, metadata practices, and analytics. Optimizes metadata pathway from provider to end user. Provides way for funders to specify what metadata they want to collect as part of research life cycle.
Proper citation: Center for Expanded Data Annotation and Retrieval (RRID:SCR_016269) Copy
https://www.phc.ox.ac.uk/research/technology-outputs/easygv
Software for calculating different measures of glycaemic variability (GV). It analyzes continuous glucose monitoring data using a simple interface.
Proper citation: easyGV (RRID:SCR_016260) Copy
http://www.nitrc.org/projects/psc/
Data analysis software that can simultaneously characterize a large number of white matter bundles within and across different subjects for group analysis. It has three major components: construction of the structural connectome for the whole brain, low-dimensional representation of streamlines in each connection, and multi-level connectome analysis.
Proper citation: Mapping Population-based Structural Connectomes (RRID:SCR_016232) Copy
Software application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences.
Proper citation: Garlic (RRID:SCR_016118) Copy
https://www.rapidnovor.com/antibody-sequencing-service/
Service for monoclonal antibody protein sequencing. It derives the sequences directly from the protein using mass spectrometry and without the need to access the cell line.
Proper citation: REmAb (RRID:SCR_016239) Copy
https://github.com/alesssia/YAMP
Software for processing and analysis of sequencing data. It has a strong focus on quality control, timely processing, functional annotation, and portability.
Proper citation: YAMP (RRID:SCR_016236) Copy
http://www.fishbrowser.org/software/LR_Gapcloser/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th, 2023. Software that uses long reads to close gaps in the assemblies.
Proper citation: LR Gapcloser (RRID:SCR_016194) Copy
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