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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | 2026-09-19 12:53:22 | 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 | 2026-09-19 12:53:21 | 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 | 2026-09-19 12:53:21 | 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 | 2026-09-19 12:53:21 | 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 | 2026-09-19 12:53:21 | 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 | 2026-09-19 12:53:21 | 106 | ||||||
|
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 | 2026-09-19 12:53:23 | 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 | 2026-09-19 12:53:25 | 26 | |||||||
|
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 | 2026-09-19 12:53:25 | 102 | |||||||||||
|
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 | 2026-09-19 12:53:25 | 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 | 2026-09-19 12:53:24 | 3 | |||||||
|
SARTools Resource Report Resource Website 100+ mentions |
SARTools (RRID:SCR_016533) | data analysis software, data processing software, software application, software resource, software toolkit | Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data. | R package, DESeq2, EdgeR, comprehensive, analysis, RNAseq, data, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: DESeq2 is related to: edgeR has parent organization: Pasteur Institute |
the France Génomique National Infrastructure | PMID:27280887 | Free, Available for download, Freely available | biotools:sartools | https://bio.tools/sartools | SCR_016533 | 2026-09-19 12:53:24 | 151 | ||||||
|
TRANSIT Resource Report Resource Website 1+ mentions |
TRANSIT (RRID:SCR_016492) | data analysis software, data processing software, software application, software resource | Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions. | statistical, analysis, TnSeq, data, identify, gene, dataset, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Texas A and M University; Texas; USA |
PMID:26447887 | Free, Available for download, Freely available | biotools:transit | https://github.com/mad-lab/transit, https://bio.tools/transit | SCR_016492 | 2026-09-19 12:53:24 | 4 | |||||||
|
PiGx Resource Report Resource Website 1+ mentions |
PiGx (RRID:SCR_016476) | PiGx | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software application as a collection of genomic pipelines used for raw fastq read data of bisulfite experiments, RNAseq samples, single cell dropseq analysis, reads from ChIPseq experiments, analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data. | collection, genomic, pipeline, bisulfite, sequencing, rnaseq, chipseq, single, cell, reproducibility, sample, analysis, mutation, data | European Union Horizon 2020 No 654248; German Federal Ministry of Education and Research (BMBF) 031 A538C RBC (de.NBI) |
Free, Available for download, Freely available | https://github.com/BIMSBbioinfo/pigx | SCR_016476 | Pipelines in Genomics | 2026-09-19 12:53:24 | 6 | |||||||
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Transcriptome Analysis Console Resource Report Resource Website 10+ mentions |
Transcriptome Analysis Console (RRID:SCR_016519) | TAC | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for microarray analysis designed for biologists . Used for identification of differential expression by providing interactive visualizations. | transcriptome, analysis, console, data, array, gene, visualization, identify | Commercially available | SCR_016519 | TAC:Transcriptome Analysis Console | 2026-09-19 12:53:24 | 21 | |||||||||
|
Viewbox4, Cephalometric software Resource Report Resource Website 1+ mentions |
Viewbox4, Cephalometric software (RRID:SCR_016481) | data analysis software, data processing software, image analysis software, software application, software resource | 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. | dHAL Software - The Company, cephalometric, analysis, rendering, viewing, measuring, data, CT scan, orthodontic, dental, skeletal, relationship, human, skull | Commercially available, Tutorial available | SCR_016481 | 2026-09-19 12:53:24 | 6 | |||||||||||
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SwarmSight Resource Report Resource Website |
SwarmSight (RRID:SCR_016451) | data analysis software, data processing software, image analysis software, software application, software resource | 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. | c language, bug, insect, antennae, proboscis, activity, research, subject, swarm, behavior, tracking, video, analysis | Free, Available for download, Acknowledgement requested | SCR_016451 | SwarmSight Software, Swarm Sight | 2026-09-19 12:53:23 | 0 | ||||||||||
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MAJIQ Resource Report Resource Website 10+ mentions |
MAJIQ (RRID:SCR_016706) | MAJIQ, | data analysis software, data processing software, software application, software resource, software toolkit | 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. | detect, quantify, local, splicing, variation, RNA-Seq, data, replicate, differential, analysis | has parent organization: University of Pennsylvania; Philadelphia; USA | NIA R01 AG046544; Penn Institute for Biomedical Informatics Pilot |
PMID:29236961 | Free, Available for download, Freely available, Tutorial available | SCR_016706 | MAJIQ, MAJIQ/Viola, Modeling Alternative Junction Inclusion Quantification | 2026-09-19 12:53:27 | 33 | ||||||
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CARD Resource Report Resource Website 10+ mentions |
CARD (RRID:SCR_016602) | CARD | analysis service resource, data analysis service, data or information resource, database, production service resource, service resource, software resource, web application | Web application for integrated analysis and interactive visualization of RNA interference (RNAi) screening data. | integrated, analysis, interactive, visualization, RNA, interfernce, screening, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Australasian Genomics Technologies Association ; Australian Cancer Research Foundation ; Australian Government’s Education Investment Fund ; Brockhoff Foundation ; Peter MacCallum Cancer Centre Foundation ; Victorian Department of Industry ; Innovation and Regional Development |
PMID:26902267 | Free, Freely available | biotools:CARD | https://bio.tools/CARD | SCR_016602 | CARD, Comprehensive Analysis of RNAi-screen Data | 2026-09-19 12:53:26 | 20 | ||||
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MetaboAnalystR Resource Report Resource Website 500+ mentions |
MetaboAnalystR (RRID:SCR_016723) | data analysis software, data processing software, data visualization software, software application, software resource | 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. | analysis, metabolomic, data, analysis, vixualization, functional, interpretation | works with: MetaboAnalyst | Canada Research Chairs ; McGill Graduate Dean Award ; Natural Sciences and Engineering Research Council of Canada |
PMID:29955821 | Free, Available for download, Freely available | SCR_016723 | 2026-09-19 12:53:28 | 525 |
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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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