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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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LabChart Reader Resource Report Resource Website 100+ mentions |
LabChart Reader (RRID:SCR_017551) | data analysis software, data processing software, software application, software resource | LabChart data analysis software creates a platform for all of your recording devices to work together, allowing you to acquire biological signals from multiple sources simultaneously and apply advanced calculations and plots as your experiment unfolds. LabChart Reader is free version of software that allows to analyse with some limitations. LabChart Reader doesn’t allow saving of data - export image only. Has data pad for analysis. | Adinstruments, LabChart, data, analysis, calculation, plot | is related to: LabChart | https://www.adinstruments.com/products/labchart/versions-and-licenses | SCR_017551 | LabChart Reader software 8.1, LabChart Reader software | 2026-09-12 12:58:54 | 144 | |||||||||
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Mesquite Resource Report Resource Website 100+ mentions |
Mesquite (RRID:SCR_017994) | data analysis software, data processing software, software application, software resource | Software tool as modular system for evolutionary analysis. Software for evolutionary biology, designed to organize and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Analyses available depend on modules installed. Comes with many packages already installed. | Modular, evolutionary, analysis, organize, comparative data, organism, phylogenetic, population genetic, non-pylogenetic | is listed by: Debian | David and Lucile Packard Foundation ; NSERC Discovery grant ; NSF ; NSF DEB 1258220 |
Free, Available for download, Freely available | https://sources.debian.org/src/mesquite/ | SCR_017994 | Mesquite 3.04, Mesquite 3.61 | 2026-09-12 12:58:56 | 183 | |||||||
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VG Studio MAX Resource Report Resource Website 10+ mentions |
VG Studio MAX (RRID:SCR_017997) | data analysis software, data processing software, data visualization software, software application, software resource | Software tool for analysis and processing of µCT data, e.g. compiling virtual 3D models of morphological structures in site by Volume Graphics GmbH. Used for visualization of CT data. | Computed tomography, CT, data, analysis, processing, 3D, visualization, CT data | Restricted | SCR_017997 | VGStudio MAX, VG Studio MAX 3.1, VGStudio | 2026-09-12 12:58:56 | 11 | ||||||||||
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HiLive Resource Report Resource Website |
HiLive (RRID:SCR_016134) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for performing read mapping that maps Illumina HiSeq sequencer read alignments when they are produced. Used in Next Generation Sequencing in time critical, clinical applications. | perform, read, mapping, sequence, alignment, analysis, Illumina, time, critical, clinical, application |
is listed by: Debian is listed by: OMICtools |
the German Federal Ministry of Health IIA5-2512-FSB-725 | PMID:27794555 | Free, Available for download | OMICS_13393 | https://sources.debian.org/src/hilive/ | https://sourceforge.net/projects/hilive/ | SCR_016134 | 2026-09-12 12:58:35 | 0 | |||||
|
jamovi Resource Report Resource Website 1000+ mentions |
jamovi (RRID:SCR_016142) | data analysis software, data processing software, software application, software resource | Software for statistical analysis and spreadsheet editing that is built on top of the R statistical language. It encourages a “community driven” philosophy, where users can develop and publish their analyses to make them available to a wide audience. | spreadsheet, r, statistic, methodology, r, package, analysis | Free, Available for download | SCR_016142 | the jamovi project | 2026-09-12 12:58:35 | 4164 | ||||||||||
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SymPhoTime 64 Resource Report Resource Website 10+ mentions |
SymPhoTime 64 (RRID:SCR_016263) | data acquisition software, data processing software, data visualization software, image acquisition software, image analysis software, software application, software resource | Software for fluorescence lifetime imaging and correlation. SymPhoTime 64 is the data acquisition software for PicoQuant's time-resolved confocal microscope MicroTime 200 and LSM upgrade kits. | fluorescent, imaging, correlation, microscope, companion software, image, analysis, microscopy, image acquisition | Commercially available, Free, Available for download | SCR_016263 | SymPhoTime | 2026-09-12 12:58:37 | 13 | ||||||||||
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Raven Resource Report Resource Website 500+ mentions |
Raven (RRID:SCR_016190) | data analysis software, data processing software, data visualization software, software application, software resource | Software for the acquisition, visualization, measurement, and analysis of sounds. Raven supports annotations for research-related analysis. | audio, sound, analysis, acquisition, visualization, bird, avian, birdsong | has parent organization: Cornell University; New York; USA | Free, Available for download, Available for purchase, Commercially available, Tutorial available | https://store.birds.cornell.edu/ProductDetails.asp?ProductCode=RAVENLITE | SCR_016190 | 2026-09-12 12:58:36 | 869 | |||||||||
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FITMASTER Resource Report Resource Website 100+ mentions |
FITMASTER (RRID:SCR_016233) | data analysis software, data processing software, software application, software resource | Software for analysis and fitting routines of electrophysiological data. Analysis can be performed on the levels of Sweeps/Traces and Series. | electrophysiology, analysis, fitting, statistic, polynomial, exponential, gaussian, boltzmann, formalism, voltage, current | Free, Available for download, Tutorial available, Demo available | SCR_016233 | HEKA FITMASTER | 2026-09-12 12:58:37 | 101 | ||||||||||
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GARLI Resource Report Resource Website 100+ mentions |
GARLI (RRID:SCR_016117) | GARLI | data analysis software, data processing software, software application, software resource | Software application for inferring phylogenetic trees and analysis of molecular sequence data using the maximum-likelihood criterion. It implements nucleotide, amino acid and codon-based models of sequence evolution. | inference, phylogenetic, tree, analysis, molecular, sequence, data, maximum, likelihood, criterion, nucleotide, amino acid, codon, model, evolution |
is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_04234 | https://code.google.com/archive/p/garli/, https://sources.debian.org/src/garli/ | SCR_016117 | Genetic Algorithm for Rapid Likelihood Inference | 2026-09-12 12:58:35 | 280 | ||||||
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Fsm-lite Resource Report Resource Website 10+ mentions |
Fsm-lite (RRID:SCR_016115) | data analysis software, data processing software, software application, software resource | Software application as a single-core implementation of frequency-based substring mining. It can be used in bioinformatics to extract substrings that discriminate two (or more) datasets inside high-throughput sequencing data. | protein, dna, rna, sequence, analysis, core, implementation, frequency, based, substring, mining, extract, discriminate, dataset, sequencing, high throughput |
is listed by: Debian is listed by: OMICtools |
Free, Available for download | OMICS_28406 | https://sources.debian.org/src/fsm-lite/ | SCR_016115 | fsm, Frequency-based String Mining, Frequency-based String Mining (lite) | 2026-09-12 12:58:35 | 19 | |||||||
|
NeuroPlex Resource Report Resource Website 100+ mentions |
NeuroPlex (RRID:SCR_016193) | data acquisition software, data analysis software, data processing software, image acquisition software, image analysis software, software application, software resource | Software for acquisition and analysis for imaging applications. The acquisition section has a variety of triggering and averaging modes, while the analysis section has extensive provisions for displaying traces (intensity vs time) and movies of propagating activity. | imaging, electrical, recording, acquisition, analysis, neuroimaging | Account required, Available for download | SCR_016193 | 2026-09-12 12:58:36 | 198 | |||||||||||
|
Glam2 Resource Report Resource Website 100+ mentions |
Glam2 (RRID:SCR_016129) | Glam2 | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software package for finding novel, gapped (recurring, variable-length patterns) motifs in related groups of DNA or protein sequences (sample output from sequences). Used to perform motif based sequence discovery for gapped motifs on DNA or protein datasets. | motif, analysis, sequence, find, amino acid, nucleotide, set, alignment, gapped, recurring, variable, letnght, pattern, DNA, protein, output, discovery, dataset | is related to: MEME Suite - Motif-based sequence analysis tools | NIGMS R01 GM103544 | PMID:18437229 | Free, Freely available for non-commercial use | http://meme-suite.org/ | SCR_016129 | Glam2: Gapped local alignment of motifs 2 | 2026-09-12 12:58:35 | 203 | |||||
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GenomeTools Resource Report Resource Website 100+ mentions |
GenomeTools (RRID:SCR_016120) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software toolkit for biological sequence analysis and -presentation combined into a single binary. It is used for genome analysis, efficient processing of structured genome annotations and contains binaries for sequence and annotation handling, sequence compression, index structure generation and access, annotation visualization. | analysis, genome, annotate, sequence, compress, visualization, single, binary, combine, structure, efficient |
is listed by: Debian is listed by: OMICtools |
PMID:24091398 | Free, Available for download | OMICS_16119 | https://sources.debian.org/src/genometools/ | SCR_016120 | GenomeTool, Genome Tools, Genome Tool | 2026-09-12 12:58:35 | 150 | ||||||
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Easy fMRI Resource Report Resource Website 1+ mentions |
Easy fMRI (RRID:SCR_016392) | data analysis software, data processing software, software application, software resource | Software that employs machine learning techniques and high-performance computing for analyzing task-based fMRI datasets. It applies Feature Analysis, Hyperalignment, Multi-voxel Pattern Analysis (MVPA), Representational Similarity Analysis (RSA), and more. | fmri, imaging, neuroimaging, analysis, fsl, scikit-learn, tensorflow, suma | Open source, Free, Available for download | https://sourceforge.net/projects/easyfmri/files/, https://github.com/easyfmri/easyfmri | SCR_016392 | easyfMRI | 2026-09-12 12:58:39 | 2 | |||||||||
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Phenocarta Resource Report Resource Website 1+ mentions |
Phenocarta (RRID:SCR_016273) | data analysis software, data or information resource, data processing software, database, software application, software resource | Database that consolidates information on genes and phenotypes across multiple resources and allows tracking and exploring of the associations. Part of Gemma, a web site, database and a set of tools for the meta-analysis, re-use and sharing of genomics data. | phenotype, meta, analysis, genome, gene, expression |
is related to: Gemma has parent organization: University of British Columbia; British Columbia; Canada |
PMID:22782548 | Free, Freely available | http://pavlab.msl.ubc.ca/software-and-resources/ | SCR_016273 | Phenocarta | 2026-09-12 12:58:37 | 2 | |||||||
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AspireDB Resource Report Resource Website |
AspireDB (RRID:SCR_016272) | data analysis software, data processing software, software application, software resource, web application | Web based software for analyzing genomic variants CNVs, SNVs, and Indels and phenotypes. It aims to represent the relationships between discovered variants and phenotypes. | gene, cnv, snv, indel, phenotype, analysis, variant | BC Knowledge Development Fund ; Canadian Foundation for Innovation |
Account required, Freely available | https://github.com/ppavlidis/aspiredb, http://pavlab.msl.ubc.ca/software-and-resources/ | SCR_016272 | 2026-09-12 12:58:37 | 0 | |||||||||
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MicroFilament Analyzer Resource Report Resource Website 1+ mentions |
MicroFilament Analyzer (RRID:SCR_016411) | MFA:MicroFilament Analyzer | data processing software, image analysis software, software application, software resource, software toolkit | Software package for image analysis to determine the orientation of filamentous structures on digital images. Used as an image‐processing tool for analyzing cytoskeleton and cellulose fiber orientation in pant imagesk. | image, analysis, determine, orientation, filamentous, structure, digital, cytoskeleton, cellulose, fiber | is related to: MATLAB | PMID:23489480 | Free, Freely available | http://www.ua.ac.be/bimef/MFA | SCR_016411 | MFA | 2026-09-12 12:58:39 | 1 | ||||||
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Fractalis Resource Report Resource Website 1+ mentions |
Fractalis (RRID:SCR_016362) | analysis service resource, data access protocol, data analysis service, data processing software, data visualization software, production service resource, service resource, software application, software library, software resource, software toolkit, web service | 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. | platform, independent, interactive, visual, analysis, biomedical, data, library | Luxembourg Ministry of Higher Education and Research ; National Centre of Excellence in Research on Parkinson’s disease NCER13/BM/11264123 |
Free, Available for download, Freely available | https://git-r3lab.uni.lu/Fractalis/fractalis/blob/master/README.md | SCR_016362 | 2026-09-12 12:58:38 | 1 | |||||||||
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Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | data analysis software, data processing software, software application, software resource, software toolkit | 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. | analysis, heterogenous, population, single, cell, gene, expression, data, large, single-cell RNA-Seq, transcriptional, regulation, heterogen | Alfred P. Sloan Foundation Research Fellowship ; NIH DP2 HD088158 |
PMID:24658644 | Free, Available for download, Freely available | SCR_016339 | Monocle 2 | 2026-09-12 12:58:38 | 227 | ||||||||
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Electrographic Seizure Analyzer Resource Report Resource Website 1+ mentions |
Electrographic Seizure Analyzer (RRID:SCR_016344) | data analysis software, data processing software, software application, software resource | Software to automate analysis of electrographic seizures based on EEG or LFP data, featuring customizable thresholds and parameters for event detection and parameter setting. | automate, analysis, electrographic, seizure, EEG, LFP, data, event, detection, parameter, setting | is related to: MATLAB | Free, Available for download, Freely available | SCR_016344 | 2026-09-12 12:58:38 | 5 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
