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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NetworkX Resource Report Resource Website 100+ mentions |
NetworkX (RRID:SCR_016864) | data processing software, software application, data analysis software, software resource, network analysis software | Software Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | create, analysis, structure, dynamic, function, complex, network, data | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/networkx/networkx | SCR_016864 | 2026-08-05 10:46:46 | 111 | |||||||||
|
Rampart Resource Report Resource Website 1+ mentions |
Rampart (RRID:SCR_016742) | data processing software, software application, workflow software, software resource | Software for workflow management system for de novo genome assembly of DNA sequence data.Designed to exploit high performance computing environments, such as clusters and shared memory systems. | workflow, management, system, de novo, genome, assembly, DNA, sequence, data, high, performance, computing, environment, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: The Genome Analysis Centre; Norwich; United Kingdom |
BBSRC | PMID:25637556 | Free, Available for download, Freely available | biotools:rampart | http://www.earlham.ac.uk/rampart/, https://bio.tools/rampart | SCR_016742 | 2026-08-05 10:46:39 | 2 | ||||||
|
riboSeqR Resource Report Resource Website 1+ mentions |
riboSeqR (RRID:SCR_016947) | software resource, data processing software, software application, data analysis software | Software tool for analysis of sequencing data from ribosome profiling experiments. Used for plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments. | analysis, sequencing, data, ribosome, profiling, experiment, plotting, function, frameshift, detect, parsing |
is listed by: Bioconductor is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_016947 | 2026-08-05 10:46:41 | 4 | ||||||||||
|
Rsubread Resource Report Resource Website 100+ mentions |
Rsubread (RRID:SCR_016945) | data processing software, image analysis software, software application, alignment software, data analysis software, software resource | Software R package for sequence alignment and counting for R. Used for analyses of second and third generation sequencing data, for read mapping, read counting, SNP calling, short and long read alignment, quantification and mutation discovery. Includes assessment of sequence reads, read alignment, read summarization, exon-exon junction detection, fusion detection, detection of short and long indels, absolute expression calling and SNP calling. Can be used with reads generated from any of the major sequencing platforms including Illumina GA/HiSeq/MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM/Proton sequencers. | sequence, alignment, counting, multi, seed, strategy, mapping, read, reference, genome, analysis, data, SNP, calling, mutation, discovery, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing is related to: Subread |
Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support ; Australian Government |
PMID:23558742 | Free, Available for download, Freely available | biotools:rsubread | https://bio.tools/rsubread | SCR_016945 | 2026-08-05 10:46:46 | 188 | ||||||
|
scran Resource Report Resource Website 50+ mentions |
scran (RRID:SCR_016944) | SCRAN | software resource, data processing software, software application, data analysis software | Software package for low-level analyses of single-cell RNA-seq data. Used for quality control, data exploration and normalization, cell cycle phase assignment, identification of highly variable and correlated genes, clustering into subpopulations and marker gene detection. | low, level, analysis, scRNA-seq, data, normalization, cell, cycle, phase, gene, variable, correlation, cluster, subpopulation, marker, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools is related to: R Project for Statistical Computing |
Cancer Research UK ; National Health and Medical Research Council of Australia ; EMBL |
PMID:27909575 | Free, Available for download, Freely available | biotools:scran | https://bio.tools/scran | SCR_016944 | Single-Cell Rna-seq data ANalysis, SCRAN | 2026-08-05 10:46:46 | 92 | ||||
|
Bulked segregation analysis tools for outbreeding species Resource Report Resource Website 1+ mentions |
Bulked segregation analysis tools for outbreeding species (RRID:SCR_017009) | BSATOS | data processing software, 1d time-series analysis software, software application, data analysis software, time-series analysis software, software resource | Software tools for next generation sequencing based bulked segregation analysis for outbreeding species including fruit trees such as apple or cirtus. Used to improve gene mapping efficiency of next generation sequencing based segregant analysis in outbreeding species and realize rapid candidate gene mining based on multi-omics data. | next, generation, sequencing, bulked, segregation, analysis, outbreeting, specie, gene, mapping, data | Free, Available for download, Freely available | SCR_017009 | Bulked segregation analysis tools for outbreeding species, Bulked Segregation Analysis Tools for Outbreeding Species, BSATOS | 2026-08-05 10:46:48 | 2 | |||||||||
|
Allen Brain Atlas Resource Report Resource Website 100+ mentions |
Allen Brain Atlas (RRID:SCR_017001) | data or information resource, portal, project portal, atlas | Portal provides access to data and web based applications created for benefit of global research community by Allen Institute for Brain Science. Projects to ombine genomics with neuroanatomy by creating gene expression maps for mouse and human brain. Mouse Brain Atlas, Human Brain Atlas, Developing Mouse Brain Atlas, Developing Human Brain Atlas, Mouse Connectivity Atlas, Non-Human Primate Atlas, and Mouse Spinal Cord Atlas and three related projects Glioblastoma, Mouse Diversity, and Sleep data banks, are used to advance various fields of science especially in neurobiological diseases. | genomic, data, neuroanatomy, gene, expression, map, mouse, human, brain, atlas, neurobiology |
is related to: Allen Software Development Kit is related to: Common Cell Type Nomenclature has parent organization: Allen Institute has parent organization: Allen Institute for Brain Science is parent organization of: Allen Mouse Brain Reference Atlas is parent organization of: Allen Human Brain Atlas is parent organization of: Allen Developing Mouse Brain Atlas is parent organization of: Allen Mouse Brain Connectivity Atlas is parent organization of: Allen Mouse Spinal Cord Atlas is parent organization of: CellTax vignette is parent organization of: Allen Brain Atlas expression map of Cre and other drivers provides: ABA Mouse Brain: Atlas works with: Transcriptomics Explorer works with: Kinase Associated Neural Phospho Signaling |
Free, Freely available | SCR_017530 | SCR_017001 | Allen Brain Atlas, Brain Atlases, Allen Mouse Brain Atlas, The Allen Brain Atlas, Allen Human Brain Atlas | 2026-08-05 10:46:41 | 195 | ||||||||
|
GenomeScope Resource Report Resource Website 500+ mentions |
GenomeScope (RRID:SCR_017014) | Genomescope | data processing software, software application, data analysis software, software resource, service resource | Open source software package for fast genome analysis from unassembled short reads. Used to estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach. | genome, unassembled, sequenced, data, short, read, analysis, heterozygosity, repeat, content, size, kmer | is related to: Cold Spring Harbor Laboratory | NSF DBI 1350041; NSF IOS 1237880; NHGRI R01 HG006677 |
PMID:28369201 | Free, Freely available, | http://qb.cshl.edu/genomescope/ | SCR_017014 | 2026-08-05 10:46:48 | 651 | ||||||
|
OmicsSIMLA Resource Report Resource Website 1+ mentions |
OmicsSIMLA (RRID:SCR_017011) | software toolkit, software application, simulation software, software resource | Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version. | multi, omics, data, simulator, disease, genomic, epigenomic, transcriptomic, proteomic, genome, sequencing, protein, RNA | is listed by: OMICtools | Ministry of Science and Technology in Taiwan | DOI:10.1101/426510 | Freely available, Available to download, Free | OMICS_31363 | SCR_017011 | 2026-08-05 10:46:47 | 1 | |||||||
|
mixOmics Resource Report Resource Website 50+ mentions |
mixOmics (RRID:SCR_016889) | software resource, data processing software, software application, data analysis software | Software R package of multivariate methods for the exploration and integration of biological datasets with a focus on variable selection. Used to analyse data from high throughput sequencing technologies and spectral imaging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | multivariate, exploration, integration, biological, dataset, variable, selection, analysis, data, high, throughput, sequencing, technology, spectral, imaging |
is related to: R Project for Statistical Computing has parent organization: University of Melbourne; Victoria; Australia |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016889 | 2026-08-05 10:46:45 | 58 | ||||||||||
|
Tools for NIfTI and ANALYZE image Resource Report Resource Website 1+ mentions |
Tools for NIfTI and ANALYZE image (RRID:SCR_016895) | data processing software, software application, image analysis software, data analysis software, software toolkit, software resource, service resource | Matlab based scripts for load, save, make, reslice, view and edit both Neuroimaging Informatics Technology Initiative (NIfTI) and ANALYZE data on any platform. | neuroimaging, data, program, analysis, image |
is related to: NIfTI Data Format Working Group is related to: MATLAB |
Free, Available for download, Freely available | https://perso.telecom-paristech.fr/bloch/P6Image/Projets/Nez2/NIfTI_matlab_tools/NIfTI_tools.pdf | SCR_016895 | Neuroimaging Informatics Technology Initiative (NIfTI) and Analyze Image data | 2026-08-05 10:46:40 | 1 | ||||||||
|
FlowSOM Resource Report Resource Website 100+ mentions |
FlowSOM (RRID:SCR_016899) | data processing software, software application, data visualization software, data analysis software, software resource | Software tool to analyze Flow or mass cytometry data using a Self-Organizing Map. Used to obtain an overview of how all markers are behaving on all cells, and to detect subsets that might be missed otherwise. | flow, cytometry, data, analysis, self, organizing, map, marker, cell, detect, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is related to: R Project for Statistical Computing is a plug in for: FlowJo |
PMID:25573116 | Free, Available for download, Freely available | biotools:flowsom | https://bioconductor.org/packages/release/bioc/html/FlowSOM.html, https://www.flowjo.com/exchange/#/plugin/profile?id=7, https://bio.tools/flowsom | SCR_016899 | FlowSOM, Flow Self Organizing Map | 2026-08-05 10:46:46 | 106 | ||||||
|
FRETBursts Resource Report Resource Website 1+ mentions |
FRETBursts (RRID:SCR_016898) | FRETBursts | data processing software, software application, data analysis software, software toolkit, software resource | Software for burst analysis of freely diffusing single-molecule Förster Resonance Energy Transfer (smFRET) experiments to study cellular processes at the molecular scale. Used for single and multi-spot single-molecule FRET (smFRET) data. | freely, diffusing, single, molecule, FRET, smFRET, cellular, process, intermolecular, interaction, conformational, change, biomacromolecule, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NIGMS R01 GM95904; NIGMS R01 GM069709 |
PMID:27532626 | Free, Available for download, Freely available | biotools:fretbursts | https://opensmfs.github.io/FRETBursts/, https://bio.tools/fretbursts | SCR_016898 | Förster Resonance Energy Transfer Bursts, FRETBursts | 2026-08-05 10:46:40 | 2 | ||||
|
CoSMoS_Analysis Resource Report Resource Website 10+ mentions |
CoSMoS_Analysis (RRID:SCR_016896) | CoSMoS Analysis | data processing software, image analysis software, software application, data analysis software, software resource | Software tools for analyzing co-localization single-molecule spectroscopy image data. | co-localization, single, molecule, spectroscopy, image, data, analysis | NIGMS ; NIH |
Free, Available for download, Freely available | SCR_016896 | co-localization single-molecule spectroscopy, Co-localization Single-Molecule Spectroscopy Analysis, co-localization single molecule spectroscopy, CoSMoS | 2026-08-05 10:46:46 | 17 | ||||||||
|
dcmqi Resource Report Resource Website 1+ mentions |
dcmqi (RRID:SCR_016933) | dcmqi | data processing software, software library, software application, software toolkit, software resource, image processing software | Software library to help with the conversion between imaging research formats and the standard DICOM representation for image analysis results. Used to implement conversion of the data stored in commonly used research formats into the standard DICOM representation. Available as a precompiled binary package for every major operating system, as a Docker image, and as an extension to 3D Slicer. | DICOM, converter, medical, image, computing, quantitative, analysis, clinical, data, metadata, radiology, standard, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Harvard University; Cambridge; United States |
NCI U24 CA180918; NIBIB P41 EB015902; NIBIB P41 EB01589; NIBIB R01 EB014955 |
PMID:29092948 | Free, Available for download, Freely available, Tutorial available | biotools:dcmqi | https://github.com/QIICR/dcmqi, https://bio.tools/dcmqi | SCR_016933 | DICOM for Quantitative Imaging, The Digital imaging and Communications in Medicine for Quantitative Imaging, Digital imaging and Communications in Medicine for Quantitative Imaging, DCMQI | 2026-08-05 10:46:46 | 3 | ||||
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Wizard Resource Report Resource Website 1+ mentions |
Wizard (RRID:SCR_016939) | software resource, data processing software, software application, data analysis software | Software tool for data analysis and exploration. Statistics software for Mac. | statistics, software, Mac, data, analysis | Commercially available, Free trial available, Tutorial available | https://www.macupdate.com/app/mac/50415/wizard | SCR_016939 | Wizard 1.9.28, Wizard 1.9.27, Wizardmac | 2026-08-05 10:46:40 | 4 | |||||||||
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International Human Epigenome Consortium Resource Report Resource Website 10+ mentions |
International Human Epigenome Consortium (RRID:SCR_016937) | IHEC | data or information resource, portal, consortium, organization portal | Consortium to coordinate epigenome mapping and characterization worldwide to avoid redundant research effort, to implement high data quality standards, to coordinate data storage, management and analysis and to provide free access to the high resolution reference human epigenome maps for normal and disease cell types to the research community. Promotes data sharing. You may view, search and download the data already released by the different IHEC associated projects via the IHEC Data Portal. | reference, human, epigenome, map, normal, disease, cell, data, quality, standard, sharing |
is related to: 4D Nucleome is related to: Canadian Epigenetics, Environment and Health Research Consortium Network is parent organization of: International Human Epigenome Consortium Data Portal |
Free access to the research community, Open and controlled access to datasets according to policies and guidelines | https://epigenomesportal.ca/ihec/ | SCR_016937 | International Human Epigenome Consortium, IHEC | 2026-08-05 10:46:46 | 26 | |||||||
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XDSME Resource Report Resource Website 10+ mentions |
XDSME (RRID:SCR_016943) | xdsme | data processing software, software application, software toolkit, software resource, image processing software | Software package of python scripts made to simplify the processing of crystal diffraction images. | simplify, processing, crystal, diffraction, image, data, XDS |
uses: Python Programming Language works with: XDS Program Package |
Free, Available for download, Freely available | SCR_016943 | XDSME, X-ray Detector Software Made Easier, XDS Made Easier | 2026-08-05 10:46:41 | 14 | ||||||||
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NetworkAnalyst Resource Report Resource Website 500+ mentions |
NetworkAnalyst (RRID:SCR_016909) | data processing software, web service, data access protocol, software application, data analysis software, software resource, network analysis software, data analysis service, production service resource, service resource, analysis service resource | Web tool for gene expression profiling, meta-analysis and systems understanding. Used for statistical, visual and network-based meta-analysis of gene expression data. | gene, expression, profiling, meta, data, analysis, statistical, visual, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:25950236 | Free, Freely available, Tutorial available | biotools:networkanalyst | https://bio.tools/networkanalyst | SCR_016909 | 2026-08-05 10:46:46 | 635 | |||||||
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ProSight Lite Resource Report Resource Website 10+ mentions |
ProSight Lite (RRID:SCR_016908) | software resource, data processing software, software application, data analysis software | Software application for matching a single candidate protein sequence and its modifications against a set of mass spectrometric observations. Used to analyze top-down mass spectrometry data. | matching, single, protein, sequence, proteomics, top-down proteomics, mass, spectrometric, data, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Northwestern University; Illinois; USA is provided by: National Resource for Translational and Developmental Proteomics |
NIGMS R01 GM067193; NIDA P30 DA018310 |
DOI:10.1002/pmic.201400313 | Free, Available for download, Freely available | biotools:prosigh_lite | https://bio.tools/prosight_lite | SCR_016908 | 2026-08-05 10:46:46 | 14 |
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