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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | ||||||||||
|
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 | ||||||
|
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 | |||||
|
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 | |||||||
|
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 | |||||||||
|
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 | ||||||
|
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 | ||||||||
|
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 | ||||||||||
|
BioJupies Resource Report Resource Website 50+ mentions |
BioJupies (RRID:SCR_016346) | software resource, web application | 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. | automatically, generate, RNAseq, data, analysis, notebook, create, visualize, report, custom, raw, processed, user, interface | is affiliated with: Icahn School of Medicine at Mount Sinai; New York; USA | Free, Available for download, Freely available | SCR_016346 | 2026-09-12 12:58:38 | 72 | ||||||||||
|
MAST Resource Report Resource Website 100+ mentions |
MAST (RRID:SCR_016340) | MAST | data analysis software, data processing software, software application, software resource, software toolkit | Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data. | model, based, analysis, single, cell, transcriptomics, RNA, sequencing, data | Bill and Melinda Gates Foundation OPP1032317; NIBIB R01 EB008400; NIH DP2 DE023321 |
DOI:10.5281/zenodo.18539 | Free, Available for download, Freely available | https://github.com/RGLab/MAST/ | SCR_016340 | Model based Analysis of Single Cell Transcriptomics | 2026-09-12 12:58:38 | 106 | ||||||
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MGnify Resource Report Resource Website 50+ mentions |
MGnify (RRID:SCR_016429) | data or information resource, data repository, portal, service resource, storage service resource | Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020. | analysis, exploration, metagenomic, metatranscriptomic, amplicon, assembly, data, sequence, ENA, microbial, population, environment, bio.tools |
is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: Debian is listed by: bio.tools is related to: NIDDK Information Network (dkNET) |
EMBL ; EU Seventh Framework Programme for Research MICROB3; InnovateUK 102513; Research Councils UK (RCUK) ; the Biotechnology and Biological Sciences Research Council (BBSRC) BBM0117551; the Biotechnology and Biological Sciences Research Council (BBSRC) BBN0183541; the Biotechnology and Biological Sciences Research Council BBI02612X1; the Biotechnology and Biological Sciences Research Council BBM0117551; the European Commission within the Research Infrastructures programme of Horizon 2020 676559 |
PMID:31696235 | Free, Freely available, Training online available | r3d100011192, biotools:MGnify | https://bio.tools/MGnify, https://doi.org/10.17616/R34W68 | SCR_016429 | , MGnify, EBI Metagenomics | 2026-09-12 12:58:39 | 74 | |||||
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Pymatgen Resource Report Resource Website 10+ mentions |
Pymatgen (RRID:SCR_016565) | Pymatgen | software library, software resource, software toolkit | Python library for materials analysis codes. Defines core object representations for structures and molecules. | material, analysis, code, core, object, representation, structure, molecule | DOI:10.1016/j.commatsci.2012.10.028 | Free, Available for download, Freely available. | https://github.com/materialsproject/pymatgen | SCR_016565 | PYthon MATerials GENomics | 2026-09-12 12:58:41 | 26 | |||||||
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MyAssays Resource Report Resource Website 100+ mentions |
MyAssays (RRID:SCR_016562) | data analysis software, data processing software, service resource, software application, software resource | Software tool for assay data analysis. | assay, data, analysis | Free, Freely available, Registration required, Tutorial available | SCR_016562 | 2026-09-12 12:58:41 | 102 | |||||||||||
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Simple Neurite Tracer Resource Report Resource Website 10+ mentions |
Simple Neurite Tracer (RRID:SCR_016566) | data analysis software, data processing software, data visualization software, image analysis software, image reconstruction software, software application, software resource | 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. | reconstruction, visualization, analysis, tube, structure, neuronal, process, blood, vessel, image | has parent organization: University of Edinburgh; Scotland; United Kingdom | BBSRC ; EPSRC ; MRC |
PMID:21727141 | Free, Available for download, Freely available | https://github.com/fiji/Simple_Neurite_Tracer/releases/tag/Simple_Neurite_Tracer-3.1.3 | SCR_016566 | 2026-09-12 12:58:41 | 40 | |||||||
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Splicing Express Resource Report Resource Website 1+ mentions |
Splicing Express (RRID:SCR_016498) | data analysis software, data processing software, data visualization software, software application, software resource | Software suite for Alternative Splicing Events (ASEs) analysis from transcriptome sequencing data in any transcriptome. Used for identification, annotation and visualization. Written in Perl and suitable to run only in UNIX-like systems. | alternative, splicing, analysis, next, generation, sequencing, data, transcriptome, identify, annotate, visualize, Perl, UNIX, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:26618088 | Free, Available for download, Freely available | biotools:splicing_express | https://bio.tools/splicing_express | SCR_016498 | 2026-09-12 12:58:40 | 3 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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