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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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UN-SCAN-IT Gel Analysis Software Resource Report Resource Website 10+ mentions |
UN-SCAN-IT Gel Analysis Software (RRID:SCR_017291) | data processing software, image analysis software, software application, software resource | Software package for densitometry measurements of electrophoresis gels by Silk Scientific Inc. Gel analysis software. Turns scanner into gel densitometer. Works with most image formats (TIFF, JPG, BMP, GIF, etc.) from any scanner, digital camera, or other image source. Can quantify Western blots, Agarose gels, PCR gels, TLC. | electrophoresis, gel, image, analysis, density, quantification, Silk Scientific Inc | Restricted | SCR_017291 | 2026-09-12 01:01:05 | 10 | |||||||||||
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SegAN Resource Report Resource Website 1+ mentions |
SegAN (RRID:SCR_016215) | data processing software, image analysis software, software application, software resource | Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps. | neural, network, segmentation, pixel, spatial, image, medical, analysis, labelling, loss function, segmentor | LHNCBC HHSN276201500692P; NIH ; NLM |
Free, Available for download | SCR_016215 | Semantic Segmentation with Adversarial Learning (SegAN), Semantic Segmentation with Adversarial Learning, SegAN: Semantic Segmentation with Adversarial Learning | 2026-09-12 01:01:04 | 4 | |||||||||
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IncuCyte® Chemotaxis Software Resource Report Resource Website 10+ mentions |
IncuCyte® Chemotaxis Software (RRID:SCR_017316) | data processing software, image analysis software, software application, software resource | IncuCyte™ Chemotaxis Cell Migration Software by Essen Bioscience. Add on software module for IncuCyte ZOOM® live cell analysis system. To analyze label free and fluorescently labeled chemotactic cell migration images acquired using ClearView Chemotaxis Plate. | Add-on, module, IncuCyte ZOOM, live-cell, analysis, system, ClearView, Chemotaxis, Plate, Essen Bioscience, Sartorius | is provided by: Sartorius | Restricted | SCR_017316 | IncuCyte Chemotaxis Software | 2026-09-12 01:01:05 | 12 | |||||||||
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cryoSPARC Resource Report Resource Website 1000+ mentions |
cryoSPARC (RRID:SCR_016501) | data processing software, image analysis software, software application, software resource | Software integrated platform used for obtaining 3D structural information from single particle cryo-EM data. Enables automated, high quality and high-throughput structure discovery of proteins, viruses and molecular complexes for research and drug discovery. | Structura Biotechnology Inc., data, processing, analysis, image, single, particle, cryo-EM, structure, discovery, automated, protein, virus, molecular, complex | is related to: University of Toronto; Ontario; Canada | PMID:28165473 | Available free of charge for academic users with a valid institutional email address, Trail available | SCR_016501 | 2026-09-12 01:01:04 | 2939 | |||||||||
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Whole Tale Resource Report Resource Website 1+ mentions |
Whole Tale (RRID:SCR_017537) | data or information resource, portal, project portal | Platform for reproducible research. Code base for publishing data. For merging science and cyberinfrastructure pathways. Data Infrastructure Building Block (DIBBS) initiative to build scalable, open source, web-based, multi-user platform for reproducible research enabling creation, publication, and execution of tales – executable research objects that capture data, code, and complete software environment used to produce research findings. To enable researchers to define and create computational environment to manage complete conduct of computational experiments and expose them for analysis and reproducibility. | Reproducible, data, merging, science, cyberinfrastructure, pathway, tale, capture, code, finding, analysis | NSF 1541450 | DOI:10.1016/j.future.2017.12.029 | Free, Freely available | https://github.com/whole-tale/wt-design-docs//blob/stable/README.rst | SCR_017537 | 2026-09-12 01:01:06 | 1 | ||||||||
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Sniffles Resource Report Resource Website 50+ mentions |
Sniffles (RRID:SCR_017619) | data processing software, software application, software resource | Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates. | Structural, variation, caller, third, generation, sequencing, SV, split, read, alignment, mismatch, region, analysis, error, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:sniffles | https://bio.tools/sniffles | SCR_017619 | 2026-09-12 01:01:06 | 76 | ||||||
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Broad Terra cloud commons for pathogen surveillance Resource Report Resource Website 10+ mentions |
Broad Terra cloud commons for pathogen surveillance (RRID:SCR_018278) | data or information resource, portal | Broad Terra cloud workspace for best practices with COVID-19 genomics data. Raw COVID-19 sequencing data from NCBI Sequence Read Archive. Workflows for genome assembly, quality control, metagenomic classification, and aggregate statistics. | COVID-19, COVID-19 data, analysis, collaborate, genomic data, sequencing data, NCBI SRA, genome assembly workflow, quality control, metagenomic classification |
is listed by: Data and Computational Resources to Address COVID-19 is listed by: Terra has parent organization: Broad Institute |
COVID-19 | Free, Freely available | SCR_018278 | Terra | 2026-09-12 01:01:07 | 39 | ||||||||
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Image Quant TL Resource Report Resource Website 100+ mentions |
Image Quant TL (RRID:SCR_018374) | data processing software, image analysis software, software application, software resource | Software tool for image analysis by Cytiva. Automated image analysis software for general purpose electrophoresis gel, blot, arrays and colony counting. | Image analysis, Cytiva, image, electrophoresis gel image, blot image, array, colony count image, analysis | SCR_018374 | , Image Quant TL array analysis, ImageQuant TL 8.2 | 2026-09-12 01:01:07 | 381 | |||||||||||
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Stereo Investigator - Whole Slide Edition Resource Report Resource Website 1+ mentions |
Stereo Investigator - Whole Slide Edition (RRID:SCR_017667) | data processing software, image analysis software, software application, software resource | Software tool for quantitative analysis using stereology on whole slide images. Used to analyze whole slide image data. Includes number, length, area and volume analyses. | Quantitative, analysis, stereology, whole, slide, image, MBF Bioscience | Restricted | SCR_017667 | 2026-09-12 01:01:06 | 3 | |||||||||||
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HALO Resource Report Resource Website 100+ mentions |
HALO (RRID:SCR_018350) | HALO | data processing software, image analysis software, software application, software resource | Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology. | Image analysis platform, digital pathology, quantitative tissue analysis, image, analysis, tissue | is listed by: SoftCite | Restricted | SCR_018350 | Indica Labs HALO software | 2026-09-12 01:01:07 | 108 | ||||||||
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Sanford Burnham Prebys Medical Discovery Institute Animal Imaging and Analysis Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Animal Imaging and Analysis (RRID:SCR_014851) | biomaterial supply resource, material resource | Animal imaging and analysis lab that provides imaging and analytical services for SBP investigators. The facility can perform in vivo non-invasive luminescence and fluorescence imaging for xenograft tumor growth and metastasis studies. Analytical equipment supports complete blood cell counts (CBC) and analysis of serum components revealing metabolic or organ stress from small samples of mouse blood. | animal, facility, imaging, analysis, in vivo, non invasive, luminescence imaging, fluorescence imaging, tumor, metastasis, complete blood cell count, cbc, serum, organic, mouse, blood | Commercially available | SCR_014851 | SBP Animal Imaging and Analysis, SBP Medical Discovery Institute Animal Imaging and Analysis | 2026-09-12 01:02:51 | 0 | ||||||||||
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QmRLFS-finder Resource Report Resource Website 10+ mentions |
QmRLFS-finder (RRID:SCR_014584) | data analytics software, software application, software resource | A software which predicts R-loop Forming Sequences (RLFSs) in nucleic acid sequences based on the experimentally supported structural models of RLFSs. The tool identifies and visualizes RLFS coordinates from natural or artificial DNA or RNA input sequences and creates standard-compliant output files for later annotation and analysis. | r-loop, r loop, rlf, rlfs, dna, rna, input sequences, output files, annotation, analysis, bio.tools |
uses: UCSC Genome Browser is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
Singapore Agency for Science Technology and Research | PMID:26400173 PMID:25883153 |
Open Source | biotools:qmrlfs-finder | https://omictools.com/qmrlfs-finder-tool, https://bio.tools/qmrlfs-finder | SCR_014584 | QmRLFS finder | 2026-09-12 01:02:51 | 16 | |||||
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eXpression2Kinases Resource Report Resource Website 1+ mentions |
eXpression2Kinases (RRID:SCR_016307) | X2K | software application, software resource | Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures. | inferred, network, transcription, factor, protein, kinase, regulate, expression, gene, analysis, combine, bio.tools |
is listed by: Debian is listed by: bio.tools |
NCRR KL2 RR029885; NIDDK P01 DK056492; NIDDK R01 DK088541; NIDDK RC4DK090860; NIGMS P50 GM071558; NLM RC2 LM010994 |
PMID:22080467 | Open source, Free, Freely available, Available for download | biotools:x2k | https://bio.tools/x2k, http://www.maayanlab.net/X2K/ | SCR_016307 | eXpression2Kinases, X2K | 2026-09-12 01:02:53 | 6 | ||||
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Metafer Resource Report Resource Website 10+ mentions |
Metafer (RRID:SCR_016306) | software application, software resource | Software application to control the slide scanning hardware in Metasystem scanning and imaging platform used for automated image analysis applications in cytogenetics, hematology, pathology, toxicology, forensic sciences or microbiology microscopy. Optimized for clinical routine. | Metasystem, slide, scanning, image, automate, analysis, microscopy, life, science | Commercially available | SCR_016306 | 2026-09-12 01:02:53 | 17 | |||||||||||
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metagear Resource Report Resource Website |
metagear (RRID:SCR_017085) | software resource, software toolkit | Software R package for research synthesis taxonomy from applying systematic review approach to assemble and screen literature, to extract data from studies, and to summarize and analyze these data with statistics of meta analysis. | sythesis, taxonomy, systematic, review, assemble, screen, literature, extract, meta, data, analysis, statistical |
is listed by: CRAN is related to: R Project for Statistical Computing has parent organization: University of South Carolina; South Carolina; USA |
NSF DBI-1262545; NSF DEB-1451031 |
DOI:10.1111/2041-210X.12472 | Free, Available for download, Freely available | https://github.com/cran/metagear, https://lajeunesse.myweb.usf.edu | SCR_017085 | 2026-09-12 01:02:54 | 0 | |||||||
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CIBERSORT Resource Report Resource Website 1000+ mentions |
CIBERSORT (RRID:SCR_016955) | data analytics software, software application, software resource | Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets. | estimation, abundance, cell, type, mixed, population, gene, expression, data, tissue, complex, analysis, RNA, biomarker, therapeutic, target, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Stanford University; Stanford; California |
B&J Cardan Oncology Research Fund ; Damon Runyon Cancer Research Foundation ; Doris Duke Charitable Foundation ; Ludwig Institute for Cancer Research ; NCI T32 CA09302; NCI U01 CA154969; NIAID U19 AI090019; Siebel Stem Cell Institute ; Thomas and Stacey Siebel Foundation ; US Department of Defense |
PMID:25822800 | Not freely available for download or distribution, Available for non commercial users, Registration required | biotools:CIbERSORt | https://bio.tools/CIBERSORT | SCR_016955 | 2026-09-12 01:02:54 | 1908 | ||||||
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Eagle Resource Report Resource Website 50+ mentions |
Eagle (RRID:SCR_015991) | software resource, software toolkit | Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods. | hmm, hidden markov model, statistic, estimation, haplotype, phase, reference, panel, sequencing, algorithm, analysis, probability |
is listed by: Debian is listed by: OMICtools has parent organization: Broad Institute |
Austrian Science Fund J-3401; Dutch Brain Foundation ; Fannie and John Hertz Foundation ; NCRR S10 RR028832; NHGRI F32HG007805; NHGRI HG007022; NHGRI R01 HG006399; NHLBI HL117626; NIMH R01 MH101244; NWO 480-05-003; Wellcome Trust WT098051 |
PMID:27694958 PMID:27270109 |
Free, Available for download, Freely available | OMICS_14099, SCR_017262 | https://sources.debian.org/src/bio-eagle/, https://github.com/poruloh/Eagle, https://data.broadinstitute.org/alkesgroup/Eagle/downloads/ | SCR_015991 | Bio-eagle, Eagle1, Eagle2 | 2026-09-12 01:02:53 | 57 | |||||
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Neurolucida Explorer Resource Report Resource Website 100+ mentions |
Neurolucida Explorer (RRID:SCR_017348) | data analytics software, software application, software resource | Companion analytical software for Neurolucida and Neurolucida 360, designed to perform extensive morphometric analysis on neuron reconstructions, serial section reconstructions, and brain maps. | Morphometric, analysis, neuron, reconstruction, section, brain, map, mbfbioscience, MBF Bioscience | SCR_017348 | 2026-09-12 01:02:54 | 116 | ||||||||||||
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Lab Streaming Layer Resource Report Resource Website 50+ mentions |
Lab Streaming Layer (RRID:SCR_017631) | LSL | software application, software resource | System for unified collection of measurement time series in research experiments that handles networking, time synchronization, near real time access as well as optionally centralized collection, viewing and disk recording of data. System for synchronizing streaming data for live analysis or recording. | Synchronizing, streaming, data, live, analysis, recording, collection, time, series, EEG | has parent organization: University of California at San Diego; California; USA | Army Research Laboratory ; NINDS R01 NS047293 |
Free, Freely available | SCR_017631 | Lab Streaming Layer | 2026-09-12 01:02:55 | 86 | |||||||
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scVelo Resource Report Resource Website 100+ mentions |
scVelo (RRID:SCR_018168) | software resource, software toolkit | Software package for estimating and analyzing RNA velocities in single cells using dynamical modeling. RNA Velocity using dynamical modeling. | RNA veloscity, analysis, single cell, dynamic modeling, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:scVelo | https://scvelo.readthedocs.io/, https://bio.tools/scVelo | SCR_018168 | scvelo, single-cell RNA Velocity generalized to transient cell states | 2026-09-12 01:02:55 | 246 |
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Data set from Kravitz, Owen and Kretizer's 2012 paper "Optogenetic identification of striatal projection neuron subtypes during in vivo recordings."
