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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MAST Resource Report Resource Website 100+ mentions |
MAST (RRID:SCR_016340) | MAST | software toolkit, software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:53 | 106 | ||||||
|
MGnify Resource Report Resource Website 50+ mentions |
MGnify (RRID:SCR_016429) | data or information resource, service resource, storage service resource, portal, data repository | 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 | 2026-08-08 12:00:54 | 74 | |||||
|
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 | 2026-08-08 12:00:58 | 26 | |||||||
|
MyAssays Resource Report Resource Website 100+ mentions |
MyAssays (RRID:SCR_016562) | software resource, software application, data analysis software, service resource, data processing software | Software tool for assay data analysis. | assay, data, analysis | Free, Freely available, Registration required, Tutorial available | SCR_016562 | 2026-08-08 12:00:58 | 102 | |||||||||||
|
Simple Neurite Tracer Resource Report Resource Website 10+ mentions |
Simple Neurite Tracer (RRID:SCR_016566) | image reconstruction software, image analysis software, software resource, software application, data analysis software, data visualization software, data processing 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 | 2026-08-08 12:00:57 | 40 | |||||||
|
Splicing Express Resource Report Resource Website 1+ mentions |
Splicing Express (RRID:SCR_016498) | software resource, software application, data analysis software, data visualization software, data processing software | 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 | 2026-08-08 12:00:32 | 3 | |||||||
|
SARTools Resource Report Resource Website 100+ mentions |
SARTools (RRID:SCR_016533) | software toolkit, software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:57 | 151 | ||||||
|
TRANSIT Resource Report Resource Website 1+ mentions |
TRANSIT (RRID:SCR_016492) | software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:55 | 4 | |||||||
|
PiGx Resource Report Resource Website 1+ mentions |
PiGx (RRID:SCR_016476) | PiGx | sequence analysis software, software toolkit, software resource, software application, data analysis software, data processing software | 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 | German Federal Ministry of Education and Research (BMBF) 031 A538C RBC (de.NBI); European Union Horizon 2020 No 654248 |
Free, Available for download, Freely available | https://github.com/BIMSBbioinfo/pigx | SCR_016476 | Pipelines in Genomics | 2026-08-08 12:00:55 | 6 | |||||||
|
Transcriptome Analysis Console Resource Report Resource Website 10+ mentions |
Transcriptome Analysis Console (RRID:SCR_016519) | TAC | sequence analysis software, software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:57 | 21 | |||||||||
|
Viewbox4, Cephalometric software Resource Report Resource Website 1+ mentions |
Viewbox4, Cephalometric software (RRID:SCR_016481) | image analysis software, software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:32 | 6 | |||||||||||
|
SwarmSight Resource Report Resource Website |
SwarmSight (RRID:SCR_016451) | image analysis software, software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:00:55 | 0 | ||||||||||
|
MAJIQ Resource Report Resource Website 10+ mentions |
MAJIQ (RRID:SCR_016706) | MAJIQ, | software toolkit, software resource, software application, data analysis software, data processing software | 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 | 2026-08-08 12:01:01 | 33 | ||||||
|
CARD Resource Report Resource Website 10+ mentions |
CARD (RRID:SCR_016602) | CARD | web application, data or information resource, production service resource, software resource, data analysis service, database, analysis service resource, service resource | 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 |
Australian Cancer Research Foundation ; Victorian Department of Industry ; Innovation and Regional Development ; Australian Government’s Education Investment Fund ; Australasian Genomics Technologies Association ; Brockhoff Foundation ; Peter MacCallum Cancer Centre Foundation |
PMID:26902267 | Free, Freely available | biotools:CARD | https://bio.tools/CARD | SCR_016602 | CARD, Comprehensive Analysis of RNAi-screen Data | 2026-08-08 12:00:58 | 20 | ||||
|
MetaboAnalystR Resource Report Resource Website 500+ mentions |
MetaboAnalystR (RRID:SCR_016723) | software resource, software application, data analysis software, data visualization software, data processing software | 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 | Natural Sciences and Engineering Research Council of Canada ; Canada Research Chairs ; McGill Graduate Dean Award |
PMID:29955821 | Free, Available for download, Freely available | SCR_016723 | 2026-08-08 12:01:00 | 525 | ||||||||
|
Particle Metrix: ZetaView Nanoparticle Tracking Analyzer Resource Report Resource Website 100+ mentions |
Particle Metrix: ZetaView Nanoparticle Tracking Analyzer (RRID:SCR_016647) | ZetaView NTA | instrument resource | Instrument for nanoparticle tracking analysis. A semi-automated method for the characterization of extracellular vesicles with associated analysis software by ParticleMetrix GmbH. | instrument, nanoparticle, tracking, analysis, ParticleMetrix GmbH, extracellular, vesicles, method | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_016647.pdf | https://partoshar.com/administrator/files/UploadFile/DLS/Zeta-View/Catalog/zetaview-en.pdf | SCR_016647 | ZetaView NTA, ZetaView Nanoparticle Tracking Analyzer | 2026-08-08 12:01:00 | 293 | ||||||||
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Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS Resource Report Resource Website 500+ mentions |
Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS (RRID:SCR_016657) | software toolkit, data acquisition software, software resource, software application, data analysis software, data analytics software, data processing software | 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. | compound, centric, data, mining, navigation, chromatic, separation, coeluting, peak, signal, noise, mass, spectrometry, analysis, qualitative |
is listed by: OMICtools is related to: Agilent Masshunter Quantitative Analysis software has parent organization: Agilent Technologies |
SCR_016657 | 2026-08-08 12:00:34 | 740 | |||||||||||
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VisR Resource Report Resource Website 1+ mentions |
VisR (RRID:SCR_016658) | VisR | software toolkit, software resource, software application, data analysis software, data visualization software, data processing software | Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses. | visual, framework, analysis, sequencing, data, dataset, integrative, interactive, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Bioconductor |
Michael Smith Foundation for Health Research ; Canadian Institutes of Health Research (CIHR) and Genome BC ; NSERC PGS-D |
PMID:26328469 | Free, Available for download, Freely available | biotools:VisR | https://bio.tools/VisR | SCR_016658 | VisRseq, VisR | 2026-08-08 12:00:59 | 5 | ||||
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IndelGenotyper Resource Report Resource Website 50+ mentions |
IndelGenotyper (RRID:SCR_016663) | GATK | sequence analysis software, software resource, software application, data analysis software, data processing software | 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. | next, generation, analysis, genomic, data, cancer, genome |
is listed by: Debian has parent organization: Broad Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | https://github.com/broadinstitute/gatk/, https://sources.debian.org/src/gatk/ | SCR_016663 | GATK Indel Genotyper, Genome Analysis Toolkit (GATK) Indel Genotyper, Indel Genotyper, GATK IndelGenotyper | 2026-08-08 12:00:59 | 88 | |||||||
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biobakery Resource Report Resource Website 10+ mentions |
biobakery (RRID:SCR_016596) | software toolkit, software resource, software application, data analysis software, data processing software | 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. | Huttenhower lab, metaomics, data, analysis, process, raw, shotgun, metagenome, metatranscriptome, sequencing, microbial, profiling, bio.tools |
is used by: Nephele is listed by: Debian is listed by: bio.tools is related to: Human Microbiome Project has parent organization: Harvard University; Cambridge; United States |
NIDDK U54 DE023798; Sloan Foundation 4406J0B; NHGRI R01 HG005220; NSF DBI1053486; NHGRI R01 HG005969; ARO W911NF1110473 |
PMID:29194469 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:biobakery | http://huttenhower.sph.harvard.edu/biobakery, https://bio.tools/biobakery | SCR_016596 | bioBakery, biobakery | 2026-08-08 12:00:59 | 18 |
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