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Software package that autonomously diagnoses rare diseases from next generation sequencing NGS data using artificial intelligence by Diploid.
Proper citation: MOON (RRID:SCR_018005) Copy
http://ultrascan.aucsolutions.com/
Software package for hydrodynamic data from analytical ultracentrifugation experiments. Features integrated data editing and analysis environment with portable graphical user interface. Provides resolution for sedimentation velocity experiments using high-performance computing modules for 2-dimensional spectrum analysis, genetic algorithm, and for Monte Carlo analysis.
Proper citation: UltraScan (RRID:SCR_018126) Copy
https://www.mbfbioscience.com/help/vesselucida-explorer/Content/VesselucidaExplorer.html
Vesselucida Explorer is Vesselucida 360 companion analysis software, to perform analyses. Provides vasculature specific metrics such as segments and nodes counts, frequency of anastomoses, vessel surface and volume, and more.
Proper citation: Vesselucida Explorer (RRID:SCR_017674) Copy
https://servicesn.mbi.ucla.edu/SAVES/
Web server for structure validation in homology modeling. Used to validate of obtained crude models. Structure analysis and validation server.
Proper citation: SAVES (RRID:SCR_018219) Copy
Web server for cancer and normal gene expression profiling and interactive analyses. Interactive web server for analyzing RNA sequencing expression data of tumors and normal samples from TCGA and GTEx projects, using standard processing pipeline. Provides customizable functions such as tumor or normal differential expression analysis, profiling according to cancer types or pathological stages, patient survival analysis, similar gene detection, correlation analysis and dimensionality reduction analysis.
Proper citation: Gene Expression Profiling Interactive Analysis (RRID:SCR_018294) Copy
https://github.com/yousra291987/ChiCMaxima
Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling.
Proper citation: ChiCMaxima (RRID:SCR_018178) Copy
http://www.innovision-systems.com/Products/MaxTraq.html
Software package for motion capture analysis by Innovision Systems Inc.
Proper citation: MaxTRAQ (RRID:SCR_018188) Copy
https://biit.cs.ut.ee/gprofiler/page/r
Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool.
Proper citation: gProfiler2 (RRID:SCR_018190) Copy
https://sedfitsedphat.nibib.nih.gov/software/default.aspx
Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.
Proper citation: SEDFIT (RRID:SCR_018365) Copy
Web platform for downstream analysis and visualization of proteomics data. Server that facilitates integrated annotation, analysis and visualization of quantitative proteomics data, with emphasis on PTM networks and integration with LINCS library of chemical and genetic perturbation signatures in order to provide further mechanistic and functional insights. Primary input for server consists of set of peptides or proteins, optionally with PTM sites, and their corresponding abundance values.
Proper citation: piNET (RRID:SCR_018693) Copy
https://cistrome.shinyapps.io/timer/
Web server for comprehensive analysis of tumor infiltrating immune cells. Web tool for systematical analysis of immune infiltrates across diverse cancer types. Allows users to input function specific parameters, with resulting figures dynamically displayed to access tumor immunological, clinical, and genomic features.
Proper citation: TIMER (RRID:SCR_018737) Copy
Web tool for analyzing regulatory potential of noncoding sequences. rVISTA web server is interconnected with TRANSFAC database, allowing users to either search for matrices present in TRANSFAC library collection or search for user defined consensus sequences. rVISTA 2.0 web server is used for high throughput discovery of cis-regulatory elements. Can process alignments generated by zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from ECR Browser and GALA database. Evolutionary analysis of transcription factor binding sites.
Proper citation: rVista (RRID:SCR_018707) Copy
Software R package for mathematical modeling of infectious disease over networks. Provides tools for simulating and analyzing mathematical models of infectious disease dynamics. Mathematical Modeling of Infectious Disease Dynamics.
Proper citation: EpiModel (RRID:SCR_018539) Copy
https://hartleys.github.io/QoRTs/
Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R.
Proper citation: QoRTs (RRID:SCR_018665) Copy
http://tools.dice-database.org/GOnet/)
Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.
Proper citation: GOnet (RRID:SCR_018977) Copy
https://github.com/LabTranslationalArchitectomics/RiboWaltz
Software R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. Works for read alignments based on transcript coordinates.
Proper citation: riboWaltz (RRID:SCR_016948) Copy
http://zhoulab.usc.edu/TopDom/
Software tool to identify Topological Domains, which are basic builiding blocks of genome structure. Detects topological domains in a linear time., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: TopDom (RRID:SCR_016964) Copy
https://github.com/ToolsVanBox/smMIPfil
Software tool for single molecule Molecular Inversion Probes data analysis. This is a stand-alone perl script. Except that this is dependent on the samtools, no installation required.
Proper citation: smMIPfil (RRID:SCR_016892) Copy
https://github.com/zitmen/thunderstorm
Software tool for automated processing, analysis, and visualization of data acquired by single molecule localization microscopy methods such as PALM and STORM. ImageJ interactive and modular plugin for SMLM data analysis and super-resolution imaging.
Proper citation: Thunder STORM (RRID:SCR_016897) Copy
http://crispr.hzau.edu.cn/CRISPR/
Web tool for synthetic single-guide RNA design of CRISPR-system in plants. Allows to search for high specificity Cas9 target sites within DNA sequences of interest, which also provides off-target loci prediction for specificity analyses and marks restriction enzyme cutting site to every sgRNA for further convenient in experiment.
Proper citation: CRISPR-P (RRID:SCR_016941) Copy
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