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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Glam2 Resource Report Resource Website 50+ mentions |
Glam2 (RRID:SCR_016129) | Glam2 | data processing software, data analysis software, software resource, sequence analysis software, software application, 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 | 2026-08-04 09:43:48 | 72 | |||||
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GenomeTools Resource Report Resource Website 100+ mentions |
GenomeTools (RRID:SCR_016120) | data processing software, data analysis software, software resource, sequence analysis software, software application, 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 | 2026-08-04 09:43:49 | 131 | ||||||
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loadGtfToGe_db Resource Report Resource Website 1+ mentions |
loadGtfToGe_db (RRID:SCR_015998) | data processing software, data visualization software, software application, software resource | One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGtfToGe_db software loads GTF files to a database for Genome Explorer. It allows the user to browse the results through the GE. | analysis, pipeline, maser, genome, explorer, upload, database, browse | Ministry of Education ; Culture ; Sports ; Science and Technology ; Japan |
Restricted | http://cell-innovation.nig.ac.jp/maser_cgi/cip-pl_list_violin_en.cgi | SCR_015998 | Management and Analysis System for Enormous Reads: loadGtfToGe_db | 2026-08-04 09:43:47 | 1 | ||||||||
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Datamash Resource Report Resource Website 1+ mentions |
Datamash (RRID:SCR_016067) | data processing software, software application, software resource, data analysis software | Software for a command-line interface which performs basic numeric, textual and statistical operations on input textual data files. It is designed to aid researchers in automating analysis pipelines, without writing code or short scripts. | command-line, interface, basic, numerical, textual, statistical, operation, input, data, files, automate, analysis, pipelines | is listed by: Debian | Free Software Foundation (FSF) | Free, Available for download | https://sources.debian.org/src/datamash/ | SCR_016067 | GNU Datamash | 2026-08-04 09:43:47 | 2 | |||||||
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Phenocarta Resource Report Resource Website 1+ mentions |
Phenocarta (RRID:SCR_016273) | data processing software, data analysis software, software resource, software application, database, data or information 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 | 2026-08-04 09:43:51 | 2 | |||||||
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AspireDB Resource Report Resource Website |
AspireDB (RRID:SCR_016272) | data processing software, data analysis software, software resource, software application, 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 | Canadian Foundation for Innovation ; BC Knowledge Development Fund |
Account required, Freely available | https://github.com/ppavlidis/aspiredb, http://pavlab.msl.ubc.ca/software-and-resources/ | SCR_016272 | 2026-08-04 09:43:52 | 0 | |||||||||
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SymPhoTime 64 Resource Report Resource Website 10+ mentions |
SymPhoTime 64 (RRID:SCR_016263) | image acquisition software, data processing software, software resource, software application, image analysis software, data visualization software, data acquisition software | 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 | 2026-08-04 09:43:52 | 13 | ||||||||||
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Raven Resource Report Resource Website 500+ mentions |
Raven (RRID:SCR_016190) | data processing software, data analysis software, software resource, software application, data visualization software | 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 | 2026-08-04 09:43:50 | 811 | |||||||||
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FITMASTER Resource Report Resource Website 50+ mentions |
FITMASTER (RRID:SCR_016233) | data processing software, software application, software resource, data analysis software | 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 | 2026-08-04 09:43:50 | 97 | ||||||||||
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NeuroPlex Resource Report Resource Website 100+ mentions |
NeuroPlex (RRID:SCR_016193) | image acquisition software, data processing software, data analysis software, software resource, software application, image analysis software, data acquisition software | 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 | 2026-08-04 09:43:49 | 194 | |||||||||||
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Fractalis Resource Report Resource Website 1+ mentions |
Fractalis (RRID:SCR_016362) | data analysis service, data processing software, analysis service resource, web service, software resource, data access protocol, software application, software library, production service resource, service resource, data visualization software, software toolkit | 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 | National Centre of Excellence in Research on Parkinson’s disease NCER13/BM/11264123; Luxembourg Ministry of Higher Education and Research |
Free, Available for download, Freely available | https://git-r3lab.uni.lu/Fractalis/fractalis/blob/master/README.md | SCR_016362 | 2026-08-04 09:43:52 | 1 | |||||||||
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Monocle2 Resource Report Resource Website 100+ mentions |
Monocle2 (RRID:SCR_016339) | data processing software, data analysis software, software resource, software application, 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 | NIH DP2 HD088158; Alfred P. Sloan Foundation Research Fellowship |
PMID:24658644 | Free, Available for download, Freely available | SCR_016339 | Monocle 2 | 2026-08-04 09:43:52 | 203 | ||||||||
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Electrographic Seizure Analyzer Resource Report Resource Website 1+ mentions |
Electrographic Seizure Analyzer (RRID:SCR_016344) | data processing software, software application, software resource, data analysis software | 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 | 2026-08-04 09:43:52 | 5 | ||||||||||
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BioJupies Resource Report Resource Website 50+ mentions |
BioJupies (RRID:SCR_016346) | web application, software resource | 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 | 2026-08-04 09:43:53 | 65 | ||||||||||
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MAST Resource Report Resource Website 50+ mentions |
MAST (RRID:SCR_016340) | MAST | data processing software, data analysis software, software resource, software application, 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 | NIH DP2 DE023321; NIBIB R01 EB008400; Bill and Melinda Gates Foundation OPP1032317 |
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 | 2026-08-04 09:43:53 | 86 | ||||||
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MGnify Resource Report Resource Website 50+ mentions |
MGnify (RRID:SCR_016429) | portal, storage service resource, data repository, service resource, data or information 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) |
the Biotechnology and Biological Sciences Research Council (BBSRC) BBM0117551; the Biotechnology and Biological Sciences Research Council (BBSRC) BBN0183541; the European Commission within the Research Infrastructures programme of Horizon 2020 676559; InnovateUK 102513; Research Councils UK (RCUK) ; EMBL ; the Biotechnology and Biological Sciences Research Council BBI02612X1; the Biotechnology and Biological Sciences Research Council BBM0117551; EU Seventh Framework Programme for Research MICROB3 |
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 | 2026-08-04 09:43:53 | 51 | |||||
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Easy fMRI Resource Report Resource Website 1+ mentions |
Easy fMRI (RRID:SCR_016392) | data processing software, software application, software resource, data analysis software | 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 | 2026-08-04 09:43:53 | 2 | |||||||||
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Pymatgen Resource Report Resource Website 10+ mentions |
Pymatgen (RRID:SCR_016565) | Pymatgen | software toolkit, software resource, software library | 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 | 2026-08-04 09:43:57 | 23 | |||||||
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MyAssays Resource Report Resource Website 50+ mentions |
MyAssays (RRID:SCR_016562) | data processing software, data analysis software, software resource, software application, service resource | Software tool for assay data analysis. | assay, data, analysis | Free, Freely available, Registration required, Tutorial available | SCR_016562 | 2026-08-04 09:43:57 | 70 | |||||||||||
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Simple Neurite Tracer Resource Report Resource Website 10+ mentions |
Simple Neurite Tracer (RRID:SCR_016566) | data processing software, data analysis software, image reconstruction software, software resource, software application, image analysis software, data visualization software | 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 | EPSRC ; MRC ; BBSRC |
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 | 2026-08-04 09:43:56 | 36 |
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