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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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NIS-Elements Resource Report Resource Website 1000+ mentions Rating or validation data |
NIS-Elements (RRID:SCR_014329) | software application, software resource, software toolkit, data analysis software, data processing software | Microscope imaging software suite used with Nikon products. NIS-Elements includes software applications for advanced and standard research, documentation, confocal microscopy, and high-content analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | element, microscope imaging software, software suite, nikon |
is listed by: SoftCite works with: Nikon ECLIPSE Ti2 inverted microscope |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014329 | Nikon Instruments Software Elements, NIS Elements, Nikon Instruments Software | 2026-02-11 10:58:54 | 3462 | |||||||||
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IMAGIC Resource Report Resource Website 100+ mentions |
IMAGIC (RRID:SCR_014447) | software application, image analysis software, software resource, data processing software, image processing software | An image analysis software that can process spectra and other multi-dimensional data-sets. The software package is aimed at processing large data sets from (cryo-) electron microscopy, especially in the field of single particle analyses. This software can be used with light and raster-tunneling microscopes, computer tomographs, FT-IR spectrometers and other signal collecting devices. This resource provides three-dimensional data processing and angular reconstitution modules that allow the three-dimensional reconstruction with point-group symmetry from the two dimensional electron microscopy projections. These models aid in the analysis of the macromolecules. | image analysis, spectra, multi-dimensional data, macromolecule, 3d processing, tomograph, spectrometer, software environment | is listed by: SoftCite | PMID:8742718 | Commercial, Account needed for download | SCR_014447 | 2026-02-11 10:58:55 | 217 | |||||||||
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LSM Image Examiner Resource Report Resource Website 1000+ mentions Rating or validation data |
LSM Image Examiner (RRID:SCR_014344) | data management software, software application, software resource | Software used to compile images obtained from the Zeiss LSM 510 confocal microscope. The browser can be used for general image archiving and handling and interactive measurement in labs and workgroups. Features include orthogonal sectioning, 3D cut function, 3D view with calculation of single projections, and interactive measurement functions in the overlay dialog, such as scale bar, distance, and area. | data management software, image archive, image management, interactive measurement | is listed by: SoftCite | Available for download | http://www.zeiss.com/microscopy/en_us/website/downloads/lsm-image-browser.html http://lsm-image-examiner.software.informer.com | SCR_014344 | LSM Image Browser | 2026-02-11 10:58:54 | 1508 | ||||||||
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MassLynx Resource Report Resource Website 5000+ mentions |
MassLynx (RRID:SCR_014271) | software application, data management software, software resource, data analysis software, data processing software, data acquisition software | Software which can acquire, analyze, manage, and share mass spectrometry data. MassLynx controls any Waters mass spectrometry system, from sample and solvent management components to mass spectrometer and auxiliary detectors. The software can acquire nominal mass, exact mass, MS/MS and exact mass MS/MS data. The software system also maintains and consolidates all user sample data. Optional Application Manager programs provide additional information for specific MS analyses and data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data acquisition software, data analysis software, data management software, mass spectrometry | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014271 | MassLynx MS Software | 2026-02-11 10:58:53 | 5802 | |||||||||
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I-TASSER Resource Report Resource Website 1000+ mentions |
I-TASSER (RRID:SCR_014627) | software resource, software application, data processing software, data analysis software | Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation. | Automated prediction, protein structure prediction, protein function prediction, protein 3D structure, amino acid sequence, alignment, simulation, 3D atomic model, protein, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: University of Michigan; Ann Arbor; USA has parent organization: University of Kansas; Kansas; USA |
NIGMS GM083107; NIGMS GM084222 |
DOI:10.1186/1471-2105-9-40 DOI:10.1093/nar/gkv342 PMID:20360767 PMID:18215316 |
Free, Available for download, Freely available | biotools:i-tasser, SCR_018803 | https://bio.tools/i-tasser | SCR_014627 | Iterative Threading Assembly Refinement, Iterative Threading ASSEmbly Refinement | 2026-02-11 10:58:59 | 3702 | |||||
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Cufflinks Resource Report Resource Website 5000+ mentions |
Cufflinks (RRID:SCR_014597) | software application, software resource, data analysis software, sequence analysis software, data processing software | Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality. | transcriptome, rna-seq, rna seq, cuffmerge, cufflink, cuffcompare, transfrags, artifacts, gtf file, transcriptome assembly, expression analysis, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite works with: GeneScissors is hosted by: GitHub |
DOI:10.1038/nbt.1621 | Acknowledgement requested, Source code available on GitHub | biotools:cufflinks, OMICS_01304, SCR_013307 | https://github.com/cole-trapnell-lab/cufflinks https://bio.tools/cufflinks https://sources.debian.org/src/cufflinks/ |
SCR_014597 | 2026-02-11 10:58:58 | 8838 | |||||||
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Minitab Resource Report Resource Website 5000+ mentions |
Minitab (RRID:SCR_014483) | software resource, software application, data processing software, data analysis software | A statistical software package that allows the user to import data, create graphs, and perform statistical analysis. It can perform basic statistical tests like descriptive statistics, hypothesis tests, confidence intervals, and normality tests as well as regression and ANOVA and quality assessment. | data analysis, statistical analysis, hypothesis, confidence, descriptive | is listed by: SoftCite | SCR_014483 | 2026-02-11 10:58:55 | 5778 | |||||||||||
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CVODE Resource Report Resource Website 50+ mentions |
CVODE (RRID:SCR_014696) | software resource, software application, data processing software, data analysis software | Solver for stiff and nonstiff ordinary differential equation (ODE) systems (initial value problem), given in explicit form y' = f(t,y), based on Adams and BDF methods. It is one of the programs that makes up the Suite of Nonlinear and Differential/Algebraic Equation Solvers (SUNDIALS)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | data analysis software, solver, equation solver, ordinary differential equation, differential equation, stiff, nonstiff | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014696 | SUNDIALS CVODE | 2026-02-11 10:59:12 | 56 | |||||||||
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MedCalc Resource Report Resource Website 10000+ mentions |
MedCalc (RRID:SCR_015044) | software resource, software application, data processing software, data analysis software | Statistical software for ROC curve analysis. MedCalc performs several statistical tests such as method comparison, method evaluation, reference intervals, and meta-analysis. | statistic, statistical analysis, roc curve, reference software | is listed by: SoftCite | Commercially available, Available for purchase, Trial available | SCR_015044 | 2026-02-11 10:59:02 | 18070 | ||||||||||
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KaleidaGraph Resource Report Resource Website 1000+ mentions |
KaleidaGraph (RRID:SCR_014980) | software application, data visualization software, software resource, data analysis software, data processing software | Data analysis, graphing, and management application that allows users to import, manipulate, analyze data, and create customized plots. Plots include x-y probability, histogram, box, percentile, horizontal bar, stack bar, column, stack column, polar, and pie. Binned data can be exported to a histogram, step plot, or spike plot. KaleidaGraph works with Windows and Macintosh systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | custom graph, custom plot, publishable graph, publishable plot, data manipulation, curve fitting | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014980 | 2026-02-11 10:59:02 | 2788 | ||||||||||
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ClustalW Resource Report Resource Website 10000+ mentions |
ClustalW (RRID:SCR_017277) | ClustalW of DDBJ | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.Web sevice of ClustalW provided by DNA data bank of Japan. | alignment, service, DNA, data, bank, Japan | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017277 | ClustalW of DNA Data Bank of Japan | 2026-02-11 10:59:39 | 10543 | ||||||||
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Pathway Commons Resource Report Resource Website 10+ mentions |
Pathway Commons (RRID:SCR_002103) | PC | data or information resource, database, software resource, web service, data access protocol | Database of publicly available pathways from multiple organisms and multiple sources represented in a common language. Pathways include biochemical reactions, complex assembly, transport and catalysis events, and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathways were downloaded directly from source databases. Each source pathway database has been created differently, some by manual extraction of pathway information from the literature and some by computational prediction. Pathway Commons provides a filtering mechanism to allow the user to view only chosen subsets of information, such as only the manually curated subset. The quality of Pathway Commons pathways is dependent on the quality of the pathways from source databases. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. It currently contains data from nine databases with over 1,668 pathways, 442,182 interactions,414 organisms and will be continually expanded and updated. (April 2013) | biological pathway, pathway, molecule, biopax, standard exchange format, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: cPath is related to: Biological General Repository for Interaction Datasets (BioGRID) is related to: IntAct is related to: Reactome is related to: MINT is related to: HumanCyc: Encyclopedia of Homo sapiens Genes and Metabolism is related to: Cancer Cell Map is related to: HPRD - Human Protein Reference Database is related to: Integrated Molecular Interaction Database is related to: Pathway Interaction Database is related to: CHEBI is related to: UniProt is related to: PANTHER is related to: WebGestalt: WEB-based GEne SeT AnaLysis Toolkit has parent organization: University of Toronto; Ontario; Canada |
NHGRI P41HG004118; NIGMS 2R01GM070743-06; NIGMS 1T32 GM083937; Cancer Biomedical Informatics Grid |
PMID:21071392 | Free, Freely available | nif-0000-20884, biotools:PathwayCommons_web_service_API | https://bio.tools/PathwayCommons_web_service_API | SCR_002103 | 2026-02-11 10:56:23 | 14 | |||||
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SAMTOOLS Resource Report Resource Website 10000+ mentions |
SAMTOOLS (RRID:SCR_002105) | SAMtools | software application, software resource, software toolkit, data analysis software, sequence analysis software, data processing software | Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data. | Samtools, BCFtools, HTSlib, next generation sequencing, nucleotide alignments, sequence variant, genomic, c, perl, read, alignment, nucleotide, sequence, data, process, sam, bam, cram, vcf, bcf, bio.tools |
is used by: deFuse is used by: Short Read Sequence Typing for Bacterial Pathogens is used by: ROSE is used by: Fcirc is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SNVer is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Platypus is related to: shovill is related to: pysam has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is parent organization of: SAMtools/BCFtools is required by: RelocaTE is required by: Wessim is required by: SL-quant is required by: smMIPfil |
Wellcome Trust ; NHGRI U54 HG002750 |
PMID:19505943 PMID:21903627 DOI:10.1093/bioinformatics/btp352 |
Free, Available for download, Freely available | SCR_018682, biotools:samtools, OMICS_01074, nlx_154607, OMICS_00090 | https://github.com/samtools/samtools https://github.com/samtools/htslib https://bio.tools/samtools https://sources.debian.org/src/samtools/ |
http://samtools.sourceforge.net/ | SCR_002105 | samtools, Samtools, Sequence Alignment Map TOOLS, SAMtools, SAM tools | 2026-02-11 10:56:25 | 30156 | |||
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Fiji Resource Report Resource Website 10000+ mentions |
Fiji (RRID:SCR_002285) | Fiji | software application, software resource, source code, data processing software, image processing software | Software package as distribution of ImageJ and ImageJ2 together with Java, Java3D and plugins organized into coherent menu structure. Used to assist research in life sciences. | imaging, microscopy, windows, linux, java, mac osx, bio.tools |
uses: Fiji/ImageJ is used by: MuscleJ is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: ImageJ is related to: SynapseLocator is related to: Golddigger is related to: Analyze Spheroid Cell Invasion In 3D Matrix has parent organization: Max Planck Institute of Molecular Cell Biology and Genetics; Dresden; Germany has plug in: BioVoxxel Toolbox has plug in: imctools has plug in: Big Data Processor has plug in: Sholl Analysis has plug in: SAIBR has plug in: TWOMBLI |
PMID:22743772 | Free, Available for download, Freely available, Acknowledgement requested | SciRes_000137, biotools:Fiji | https://github.com/fiji/fiji https://bio.tools/Fiji |
SCR_002285 | Fiji is just ImageJ | 2026-02-11 10:56:26 | 37202 | |||||
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JCB DataViewer Resource Report Resource Website 10+ mentions |
JCB DataViewer (RRID:SCR_002633) | JCB DataViewer | data repository, data or information resource, database, image repository, service resource, storage service resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 14,2026. A web-based, multi-dimensional image data-viewing application for original microscopy image datasets associated with articles published in The Journal of Cell Biology, a peer-reviewed journal published by The Rockefeller University Press. The JCB DataViewer can host multidimensional fluorescence microscopy images, 3D tomogram data, very large (gigapixel) images, and high content imaging screens. Images are presented in an interactive viewer, and the scores from high content screens are presented in interactive graphs with data points linked to the relevant images. The JCB DataViewer uses the Bio-Formats library to read over 120 different imaging file formats and convert them to the OME-TIFF image data standard. Image data are archived by the Journal and may be freely accessed by readers using the JCB DataViewer. Download of author-provided image data and associated metadata in OME-TIFF format is also possible with author permission, allowing for independent analysis of image data irrespective of acquisition or viewing software. Although the JCB DataViewer is designed to host and facilitate sharing and analysis of original microscopy image data, authors may also upload other types of original image data as supplements to their manuscripts, including histology and electron micrographs and digital scans of gels or blots. | microscopy, standardization, data sharing, archiving, data management, metadata standard, visualization, analysis, image collection, histology, electron micrograph, digital scan, gel, blot |
is listed by: FORCE11 is listed by: SoftCite is related to: OME-TIFF Format has parent organization: Rockefeller University; New York; USA |
Glencoe Software ; OME - Open Microscopy Environment |
PMID:22869591 | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_156057, r3d100010895 | https://doi.org/10.17616/R3PW4G | SCR_002633 | 2026-02-11 10:56:36 | 14 | |||||
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BLASTN Resource Report Resource Website 10000+ mentions |
BLASTN (RRID:SCR_001598) | BLASTn | production service resource, data or information resource, database, data analysis service, service resource, analysis service resource | Web application to search nucleotide databases using a nucleotide query. Algorithms: blastn, megablast, discontiguous megablast. | nucleotide, alignment, compare, sequence, genome, blast, transcript, dna sequence |
is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI works with: Seek and Blastn works with: RMBlast |
PMID:17666756 PMID:18567917 |
Free, Freely available | nlx_153932, OMICS_00990 | http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome | SCR_001598 | NCBI BLASTN, Nucleotide Blast, Standard Nucleotide BLAST | 2026-02-11 10:56:16 | 19679 | |||||
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Sequencher Resource Report Resource Website 1000+ mentions |
Sequencher (RRID:SCR_001528) | Sequencher sequence analysis software | software application, software resource, data analysis software, sequence analysis software, data processing software | Software for Next-Generation DNA sequencing, Sanger DNA analysis, and RNA sequencing. It contains sequence analysis tools which include reference-guided alignments, de novo assembly, variant calling, and SNP analyses. It has integrated the Cufflinks suite for in-depth transcript analysis and differential gene expression of RNA-Seq data. | dna, sequencing, sequence analysis software, NGS, sanger, data visualization |
is listed by: OMICtools is listed by: SoftCite |
Available for download | OMICS_01817 | http://genecodes.com/sequencher-features | SCR_001528 | Sequencher sequence analysis software | 2026-02-11 10:56:15 | 4965 | ||||||
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GenABEL Resource Report Resource Website 500+ mentions |
GenABEL (RRID:SCR_001842) | software resource, software toolkit, software library | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. R software library for genome-wide association analysis for quantitative, binary and time-till-event traits. | r, genome-wide association, single nucleotide polymorphism |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: Debian is listed by: SoftCite |
Centre for Medical Systems Biology; Netherlands ; Netherlands Genomics Initiative ; Netherlands Organisation for Scientific Research ; Russian Foundation for Basic Research |
PMID:17384015 DOI:10.1186/1471-2105-11-134 DOI:10.1093/bioinformatics/btm108 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154328, OMICS_00234 | http://mga.bionet.nsc.ru/~yurii/ABEL/GenABEL/ https://cran.r-project.org/web/packages/GenABEL/index.html https://sources.debian.org/src/probabel/ |
SCR_001842 | GenABEL package, R/GENABEL | 2026-02-11 10:56:19 | 506 | |||||
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FreeSurfer Resource Report Resource Website 10000+ mentions |
FreeSurfer (RRID:SCR_001847) | FreeSurfer | software application, image analysis software, data visualization software, software resource, data processing software | Open source software suite for processing and analyzing human brain MRI images. Used for reconstruction of brain cortical surface from structural MRI data, and overlay of functional MRI data onto reconstructed surface. Contains automatic structural imaging stream for processing cross sectional and longitudinal data. Provides anatomical analysis tools, including: representation of cortical surface between white and gray matter, representation of the pial surface, segmentation of white matter from rest of brain, skull stripping, B1 bias field correction, nonlinear registration of cortical surface of individual with stereotaxic atlas, labeling of regions of cortical surface, statistical analysis of group morphometry differences, and labeling of subcortical brain structures.Operating System: Linux, macOS. | processing, analysis, human, brain, MRI, image, reconstruction, cortical, surface, fMRI, data |
is used by: Wisconsin Cortical Thickness Analysis (CTA) Toolbox is used by: freesurfR is used by: Automatic Analysis is used by: NHP Freesurfer is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: Debian is listed by: SoftCite is related to: PySurfer is related to: RFT FDR is related to: FMRLAB is related to: TRACULA is related to: BASH4RfMRI has parent organization: Harvard University; Cambridge; United States has plug in: JOSA works with: NIAG Addiction Data |
NCRR U24 RR021382; NINDS R01 NS052585; NCRR RR014075 |
PMID:22248573 | Free, Available for download, Freely available | nif-0000-00304 | https://sources.debian.org/src/freesurfer/ http://www.nitrc.org/projects/freesurfer http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall |
SCR_001847 | 2026-02-11 10:56:20 | 11817 | |||||
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PLINK Resource Report Resource Website 10000+ mentions Issue |
PLINK (RRID:SCR_001757) | software application, software resource, software toolkit, data analysis software, data processing software | Open source whole genome association analysis toolset, designed to perform range of basic, large scale analyses in computationally efficient manner. Used for analysis of genotype/phenotype data. Through integration with gPLINK and Haploview, there is some support for subsequent visualization, annotation and storage of results. PLINK 1.9 is improved and second generation of the software. | gene, genetic, genomic, genotype, phenotype, copy number variant, whole-genome association, population, linkage analysis, whole-genome association study, data management, summary statistics, population stratification, association analysis, identity-by-descent estimation |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: SoftCite is related to: Whap is related to: PLINK/SEQ is related to: Haploview is related to: MendelIHT.jl |
PMID:17701901 DOI:10.1086/519795 |
Free, Available for download, Freely Available | nlx_154200, OMICS_00206, SCR_021271 | https://zzz.bwh.harvard.edu/plink/ https://www.cog-genomics.org/plink/1.9/general_usage#cite https://sources.debian.org/src/plink/ |
http://pngu.mgh.harvard.edu/~purcell/plink/ | SCR_001757 | PLINK 1.9, PLINK/SEQ, plink - Whole genome association analysis toolset | 2026-02-11 10:56:18 | 15344 |
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