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Software tool for microarray analysis designed for biologists . Used for identification of differential expression by providing interactive visualizations.
Proper citation: Transcriptome Analysis Console (RRID:SCR_016519) Copy
https://fractalis.lcsb.uni.lu/
Software as a scalable open-source service for platform-independent interactive visual analysis of biomedical data. It is a service and a library that work in tandem to equip existing platforms with visual analytical capabilities for explorative data analysis.
Proper citation: Fractalis (RRID:SCR_016362) Copy
http://www.dhal.com/viewboxindex.htm
Software for cephalometric analysis. Customizable. Allows rendering, viewing and measuring of 3D data from CT scanners. Used in orthodontic departments for analysis of the dental and skeletal relationships of a human skull.
Proper citation: Viewbox4, Cephalometric software (RRID:SCR_016481) Copy
Software for video analysis with modules to track insect antenna and proboscis movements. Its purpose is to assess the aggregate movement or activity levels of groups or swarms of animals.
Proper citation: SwarmSight (RRID:SCR_016451) Copy
http://cole-trapnell-lab.github.io/monocle-release/docs/
Software package for analyzing single cell gene expression, classifying and counting cells, performing differential expression analysis between subpopulations of cells, and reconstructing cellular trajcectories. Works well with very large single-cell RNA-Seq experiments containing tens of thousands of cells or more. Used in computational analysis of gene expression data in single cell gene expression studies to profile transcriptional regulation in complex biological processes and highly heterogeneous cell populations.
Proper citation: Monocle2 (RRID:SCR_016339) Copy
https://github.com/KM-Lab/Electrographic-Seizure-Analyzer
Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting.
Proper citation: Electrographic Seizure Analyzer (RRID:SCR_016344) Copy
https://amp.pharm.mssm.edu/biojupies/
Software as an open source web server that automatically generates RNA-seq data analysis of jupyter notebooks. It allows creation and containment of documents that have live code, visualizations and narrative text.
Proper citation: BioJupies (RRID:SCR_016346) Copy
https://bioconductor.org/packages/release/bioc/html/MAST.html
Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.
Proper citation: MAST (RRID:SCR_016340) Copy
Software package to detect and quantify local splicing variations (LSV) from RNA-Seq data. Used to automatically detect and downweight outliers in RNA-Seq datasets with replicates for differential splicing (SD) analysis.
Proper citation: MAJIQ (RRID:SCR_016706) Copy
Python library for materials analysis codes. Defines core object representations for structures and molecules.
Proper citation: Pymatgen (RRID:SCR_016565) Copy
Software tool for assay data analysis.
Proper citation: MyAssays (RRID:SCR_016562) Copy
Web application for integrated analysis and interactive visualization of RNA interference (RNAi) screening data.
Proper citation: CARD (RRID:SCR_016602) Copy
https://github.com/xia-lab/MetaboAnalystR
Software R package for comprehensive analysis of metabolomics data. Contains the R functions and libraries underlying MetaboAnalyst web server, including functions for metabolomic data analysis, visualization, and functional interpretation.
Proper citation: MetaboAnalystR (RRID:SCR_016723) Copy
http://imagej.net/Simple_Neurite_Tracer
Software tool for reconstruction, visualization and analysis of neuronal processes .Fiji's framework for semi-automated tracing of neurons and other tube-like structures (blood vessels) through 3D image stacks.
Proper citation: Simple Neurite Tracer (RRID:SCR_016566) Copy
Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise.
Proper citation: Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS (RRID:SCR_016657) Copy
https://visrsoftware.github.io/
Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses.
Proper citation: VisR (RRID:SCR_016658) Copy
https://software.broadinstitute.org/gatk/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer.
Proper citation: IndelGenotyper (RRID:SCR_016663) Copy
https://bitbucket.org/biobakery/biobakery/wiki/Home
Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: biobakery (RRID:SCR_016596) Copy
https://github.com/vaklip/rsfmri_fconn
Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity.
Proper citation: rsfMRI_fconn calculation (RRID:SCR_016591) Copy
Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics.
Proper citation: PhenoMeNal (RRID:SCR_016605) Copy
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