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http://snf-515788.vm.okeanos.grnet.gr/
Web tool for integrating human and mouse microRNAs in pathways.Pathway analysis web-server, providing statistics, while being able to accommodate advanced pipelines. Web server for assessment of miRNA regulatory roles and identification of controlled pathways. Supports all analyses for KEGG molecular pathways and Gene Ontology (GO) in seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Caenorhabditis elegans, Gallus gallus and Danio rerio).DIANA miRPath v.2.0 includes investigating combinatorial effect of microRNAs in pathways.DIANA-miRPath v3.0 includes deciphering microRNA function with experimental support., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: DIANA-mirPath (RRID:SCR_017354) Copy
http://pathwaynet.princeton.edu/
Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.
Proper citation: PathwayNet (RRID:SCR_017353) Copy
http://neuroproteomics.scs.illinois.edu/microMS.htm
Software Python platform for image guided Mass Spectrometry profiling. Provides graphical user interface for automatic cell finding and point based registration from whole slide images. Simplifies single cell analysis with feature rich image processing.
Proper citation: microMS (RRID:SCR_017443) Copy
http://relacs.sourceforge.net/
Software platform for closed loop data acquisition, online analysis, and stimulus generation specifically designed for, but not limited to, electrophysiological recordings.
Proper citation: Relacs (RRID:SCR_017280) Copy
https://www.mbfbioscience.com/vesselucida360
Software tool for visualization and automatic reconstruction of microvascular networks in 3D environment with built-in analysis tools by MBF Bioscience.
Proper citation: Vesselucida 360 (RRID:SCR_017320) Copy
Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses.
Proper citation: trimAl (RRID:SCR_017334) Copy
https://arxiv.org/abs/1308.2012
Software tool for estimation of genomic characteristics by analyzing k-mer frequency in de novo genome projects. Used as general and assembly independent method for estimating genomic characteristics.
Proper citation: GCE (RRID:SCR_017332) Copy
https://www.cmrr.umn.edu/downloads/mrspa
Software package to post process MR spectroscopy data. Magnetic Resonance signal processing and analysis software. Runs under Matlab.
Proper citation: MRspa (RRID:SCR_017292) Copy
https://github.com/NHLBI-BCB/IKAP
Software tool for identifying K mAjor cell population groups in single-cell RNA-seq analysis. Algorithm identifying major cell groups that improves differentiating by tuning parameters for clustering. Using multiple datasets improves identification of major cell types and facilitates cell ontology curation.
Proper citation: IKAP (RRID:SCR_017417) Copy
https://bioconductor.org/packages/release/bioc/html/Glimma.html
Software package for interactive graphics for gene expression analysis. Generates interactive visualisations for analysis of RNA-sequencing data.
Proper citation: Glimma (RRID:SCR_017389) Copy
https://sites.google.com/site/tdtdecodingtoolbox/
Software Matlab toolbox for multivariate analysis of functional and structural MRI data. Software package for multivariate analyses of functional imaging data.
Proper citation: The Decoding Toolbox (RRID:SCR_017424) Copy
Software package for advanced Bayesian evolutionary analysis by sampling trees. Used for phylogenetics, population genetics and phylodynamics. Program for Bayesian phylogenetic analysis of molecular sequences. Estimates rooted, time measured phylogenies using strict or relaxed molecular clock models. Framework can be extended by third parties. Comprised of standalone programs including BEAUti, BEAST, MASTER, RBS, SNAPP, MultiTypeTree, BDSKY, LogAnalyser, LogCombiner, TreeAnnotator, DensiTree and package manager.
Proper citation: BEAST2 (RRID:SCR_017307) Copy
https://github.com/ISUgenomics/SequelQC
Software tool that calculates key statistics and generates publication quality plots for raw PacBio Sequel data. Open source software for analyzing PacBio Sequel raw sequence data.
Proper citation: SequelQC (RRID:SCR_017279) Copy
Software tool for data analysis and scientific visualization by IONDEV SRL.
Proper citation: QtiPlot (RRID:SCR_017311) Copy
Software JAVA based application for basic analysis of Small Angle X-ray Scattering datasets.
Proper citation: SCÅTTER (RRID:SCR_017271) Copy
Portal for identifying genetic and pharmacologic dependencies and biomarkers that predicts them by providing access to datasets, visualizations, and analysis tools that are being used by Cancer Dependency Map Project at Broad Institute. Project to systematically identify genes and small molecule dependencies and to determine markers that predict sensitivity. All data generated by DepMap Project are available to public under CC BY 4.0 license on quarterly basis and pre-publication.
Proper citation: Cancer Dependency Map Portal (RRID:SCR_017655) Copy
https://deepblue.mpi-inf.mpg.de/
Central data access hub for large collections of epigenomic data. It organizes data from different sources using controlled vocabularies and ontologies. Data Server for storing, organizing, searching, and retrieving genomic and epigenomic data, handling associated metadata, and to perform different types of analysis.
Proper citation: Deep Blue Epigenomic Data Server (RRID:SCR_017490) Copy
Software for organizing and analyzing blot and gel images captured on iBright Imaging Systems. Available as desktop version PC and Mac OS compatible and cloud-based version accessible via web browser through Connect platform.
Proper citation: iBright Analysis Software (RRID:SCR_017632) Copy
http://mordred.bioc.cam.ac.uk/~rapper/rampage.php
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 23,2021.Web based structural analysis tool for any uploaded PDB file, producing Ramachandran plots, computing dihedral angles and extracting sequence from PDB. Used to visualize dihedral angles ψ against φ of amino acid residues in protein structure.
Proper citation: RAMPAGE (RRID:SCR_017590) Copy
Software Java tool for quantitative analysis of behavior. Used to address any theoretical problem that requires complex sequence of actions to be scored by human observer. Runs on microcomputer providing Java Virtual Machine[TM] and has been tested on Windows[TM] and Macintosh[TM] systems. Legacy version (version 0.9) works on older systems (Macintosh OS-9 and Windows-98), while Version 1.0 works well on Macintosh OS-X and Windows XP systems. JWatcher Video works best on Windows XP systems and has reduced functionality running in Macintosh OS-X. JWatcher-Palm can be used to acquire data on Palm OS[TM] equipped device and analyze it on your main computer.
Proper citation: JWatcher (RRID:SCR_017595) Copy
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