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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Skyline Resource Report Resource Website 1000+ mentions |
Skyline (RRID:SCR_014080) | software application, software resource, data analysis software, data processing software | Software tool as Windows client application for targeted proteomics method creation and quantitative data analysis. Open source document editor for creating and analyzing targeted proteomics experiments. Used for large scale quantitative mass spectrometry studies in life sciences. | Proteomics, SRM, MRM, DDA, DIA, shotgun, mass, spectrometry, data, analysis, quantitative |
uses: MSstats is related to: ProteoWizard has parent organization: University of Washington; Seattle; USA works with: PanoramaWeb |
NCI U24 CA126479; NIDDK R01 DK069386; NCRR P41 RR011823; NIA P30 AG013280; NHLBI R01 HL082747 |
PMID:20147306 | Free, Available for download, Freely available | SCR_014080 | 2026-07-28 09:43:23 | 2805 | ||||||||
|
Origin Resource Report Resource Website 10000+ mentions |
Origin (RRID:SCR_014212) | software application, data analysis software, software resource, data processing software, data visualization software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on December 4, 2025.Software application for data analysis and graphing. Origin contains a variety of different graph types, including statistical plots, 2D and 3D vector graphs, and counter graphs. More advance version is OriginPro which offers advanced analysis tools and Apps for Peak Fitting, Surface Fitting, Statistics and Signal Processing. | data, analysis, software, authoring, tool, scripting, graphing, statistical, publication |
is listed by: SoftCite is related to: OriginPro |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_015636 | https://www.originlab.com/index.aspx?go=PRODUCTS&PID=1834 | SCR_014212 | OriginPro | 2026-07-28 09:43:25 | 13956 | |||||||
|
Maple Resource Report Resource Website 100+ mentions |
Maple (RRID:SCR_014449) | software application, software resource, data analysis software, data processing software | Mathematical software that can compute both numeric and symbolic solutions. It can be used to analyze, explore, visualize, and solve mathematical problems. | math, analysis, mathmatics, computation, meta-analysis, numeric, symbolic | SCR_014449 | Maple Software, Maplesoft, Maple Soft, MapleSoft | 2026-07-28 09:43:26 | 148 | |||||||||||
|
Wolfram Mathematica Resource Report Resource Website 100+ mentions |
Wolfram Mathematica (RRID:SCR_014448) | software application, data processing software, software resource, data visualization software, data analytics software, data storage software | A technical computing software and computing environment that provides users with algorithms and mathematical functions for various projects and purposes. The resource incorporates other Wolfram products such as Wolfram Algorithmbase, Wolfram Language, and Wolfram Knowledgebase. | analysis, computing, machine learning, wolfram notebook, meta-algorithm, cloud | Commercial product | SCR_014448 | 2026-07-28 09:43:52 | 488 | |||||||||||
|
VolView Resource Report Resource Website 50+ mentions |
VolView (RRID:SCR_014569) | software application, data or information resource, software resource, data processing software, image processing software, image, 3d spatial image, image analysis software | A software for volume visualization that can be used by researchers to explore and analyze medical and scientific data. This software uses a variety of tools to load and visualize the data on either a 2D or 3D display. Theses tools include volume rendering, maximum intensity projections and oblique reformatting. Visualizations can be saved mid-session and be reopened at a later time. | volume visualization, volume, analysis, 2d, 3d, volume, rendering, intensity, oblique reformatting, visualization, volume rendering, rendering software |
uses: VTK has parent organization: Kitware |
Open Source | SCR_014569 | 2026-07-28 09:43:53 | 61 | ||||||||||
|
FactoMineR Resource Report Resource Website 1000+ mentions |
FactoMineR (RRID:SCR_014602) | software application, software resource, data analysis software, data processing software | Software R package for multivariate analysis which takes into account different types of data structure. Data can be organized in groups of variable, groups of individuals, or into hierarchy of variables. | multivariate, analysis, data, structure, organized, group, variable, individual, hierarchy |
is used by: ClustVis is listed by: CRAN |
https://cran.r-project.org/web/packages/FactoMineR/index.html, https://github.com/husson/FactoMineR | SCR_014602 | factominer | 2026-07-28 09:43:32 | 2349 | |||||||||
|
FastQC Resource Report Resource Website 10000+ mentions Rating or validation data |
FastQC (RRID:SCR_014583) | software application, data analysis software, software resource, data management software, data processing software | Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis. | quality control, sequence data, sequencing, analysis, data quality, pipeline, raw sequence data, modular set, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Open source, Available for download | biotools:fastqc, SCR_005539, OMICS_01043 | https://omictools.com/fastqc-tool, https://bio.tools/fastqc, https://sources.debian.org/src/fastqc/ | SCR_014583 | FastQC v0.11.5 | 2026-07-28 09:43:54 | 18745 | |||||||
|
OmniPlex Software Resource Report Resource Website 10+ mentions |
OmniPlex Software (RRID:SCR_014803) | software application, data processing software, software resource, data visualization software, data acquisition software | Neural data acquisition software for signal visualization in neuron recordings along with spike wave-form classification methods. It is made up of the PlexControl software program and the OmniPlex Server. | software, neural, neuron data, analysis, pca, data acquisition, signal visualization | Commercially available | SCR_014803 | 2026-07-28 09:43:33 | 25 | |||||||||||
|
Sanford Burnham Prebys Medical Discovery Institute Bioinformatics and Data Management Facility Resource Report Resource Website |
Sanford Burnham Prebys Medical Discovery Institute Bioinformatics and Data Management Facility (RRID:SCR_014868) | SBP MDI Bioinformatics and Data Management Facility, SBP Medical Discovery Institute Bioinformatics and Data Management Facility, SBP MDI Bioinformatics and Data Management Facility | service resource, group, training core facility, software resource, computational hosting, access service resource, core facility | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on 11132025. Facility that provides database development and management and bioinformatic network building services by utilizing on-site hardware and software. Three members of the facility are available to assist researchers with advanced bioinformatics and biostatistics analysis to help put data into biological context across various disease areas to create testable hypotheses and understand biology of the process. The bulk of support includes connecting functional genomic data with pathways and networks, connecting gene/protein expression and disease state and consultations on statistical aspects of the research with the team statistician. | data, management, database, bioinformatic, network, connectivity, statistics, analysis, biostatistics, pipeline, software | THIS RESOURCE IS NO LONGER IN SERVICE. | SCR_014868 | SBP, , Data Management Facility, MDI, Medical Discovery Institute, Sanford Burnham Prebys, Bioinformatics | 2026-07-28 09:43:34 | 0 | |||||||||
|
HeteroAnalysis Resource Report Resource Website 50+ mentions |
HeteroAnalysis (RRID:SCR_014991) | software application, data analysis software, algorithm resource, software resource, data processing software | Software for analyzing sedimentation equilibrium (SE) data from analytical ultracentrifugation experiments. It uses a model-dependent simulation of data for matching data in order to determine when equilibrium has been achieved. | sedimentation equilibrium, ultracentrifugation, analysis, model dependent | has parent organization: University of Connecticut; Connecticut; USA | Available for download | http://core.uconn.edu/files/auf/ha-help/HA-Help.htm | SCR_014991 | HeteroAnalysis Version 1.1.0.58 | 2026-07-28 09:43:36 | 62 | ||||||||
|
NetPyNE Resource Report Resource Website 10+ mentions |
NetPyNE (RRID:SCR_014758) | software application, data analysis software, software resource, data processing software, network analysis software | Software Python package for simulation and analysis of neuronal networks using the NEURON simulator.Used to facilitate development, parallel simulation, analysis, and optimization of biological neuronal networks. | Simulation, analysis, neuronal, network, NEURON, simulator, BRAIN Initiative |
uses: Python Programming Language is recommended by: BRAIN Initiative works with: NEURON |
NIBIB EB022903 | DOI:10.7554/eLife.44494.001 | Free, Available for download, Freely available | http://www.neurosimlab.org/netpyne/overview.html | SCR_014758 | Network development Python package for NEURON | 2026-07-28 09:43:35 | 26 | ||||||
|
Bowtie 2 Resource Report Resource Website 1000+ mentions |
Bowtie 2 (RRID:SCR_016368) | software application, data analysis software, sequence analysis software, software resource, data processing software, alignment software, image analysis software | Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method. | sequence, analysis, long, reference, sequence, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools |
is used by: HLA-HD is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Bowtie |
NHGRI R01 HG006102; NIGMS R01 GM083873 |
PMID:22388286 | Free, Available for download, Freely available | biotools:bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml, https://github.com/BenLangmead/bowtie2, https://bio.tools/bowtie2 | SCR_016368 | , bowtie 2, bowtie2 v 2.2.3 | 2026-07-28 09:43:31 | 1745 | |||||
|
RTCA Software Resource Report Resource Website 10+ mentions |
RTCA Software (RRID:SCR_014821) | software application, data analysis software, software resource, data processing software, data acquisition software | Data acquisition and analysis software used for xCELLigence Real Time Cell Analysis SP, DP and MP instruments. The software is used to program and execute experiments and analyze data. | system management software, cell, analysis, real time, data acquisition, data analysis | Commercially available | SCR_014821 | Real Time Cell Analysis (RTCA) Software, Real Time Cell Analysis Software, RTCA 2.0 Software | 2026-07-28 09:43:36 | 23 | ||||||||||
|
CellProfiler Image Analysis Software Resource Report Resource Website 1000+ mentions |
CellProfiler Image Analysis Software (RRID:SCR_007358) | software application, image analysis software, software resource, data processing software | Software tool to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types. | high-throughput, high content imaging, software, image, cell, phenotype, measurement, subcellular, intensity, size, shape, analysis, algorithm |
is listed by: Debian is related to: CellProfiler Analyst has parent organization: Broad Institute |
NIGMS R01 GM089652; NIGMS RC2 GM092519; NHGRI RL1 HG004671 |
PMID:21349861 PMID:17076895 PMID:19014601 PMID:19188593 |
Free, Available for download, Freely available | SCR_010649, nlx_66812, nif-0000-00280 | https://sources.debian.org/src/cellprofiler/ | SCR_007358 | Cell Profiler, CellProfiler - cell image analysis software | 2026-07-28 09:41:45 | 3265 | |||||
|
MarsBaR region of interest toolbox for SPM Resource Report Resource Website 1000+ mentions |
MarsBaR region of interest toolbox for SPM (RRID:SCR_009605) | MarsBaR | software application, software toolkit, software resource, data processing software | A toolbox for SPM which provides routines for region of interest analysis. Features include region of interest definition, combination of regions of interest with simple algebra, extraction of data for regions with and without SPM preprocessing (scaling, filtering), and statistical analyses of ROI data using the SPM statistics machinery. | analyze, linear, matlab, magnetic resonance, nifti, os independent, regression, statistical operation, region of interest, spm, analysis |
is used by: BetA-Series COrrelation is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: SPM has parent organization: SourceForge |
GNU General Public License | nlx_155806 | http://www.nitrc.org/projects/marsbar | SCR_009605 | MARSeille Boite A Region dInteret, MARSeille Boite a Region dInteret | 2026-07-28 09:42:20 | 1266 | ||||||
|
Open Babel Resource Report Resource Website 50+ mentions |
Open Babel (RRID:SCR_014920) | software application, data analytics software, software resource, data processing software | Software toolbox that is used to convert, analyze, or store data from molecular modeling, chemistry, biochemistry and other related areas. This software is used to read, write, and convert into over 110 chemical file formats. | toolbox, conversion, analysis, molecular model, chemistry, biochemistry, chemical file, bio.tools |
is listed by: bio.tools is listed by: Debian |
Open source | biotools:open_babel | https://bio.tools/open_babel | SCR_014920 | 2026-07-28 09:43:56 | 81 | ||||||||
|
Whole Tale Resource Report Resource Website 1+ mentions |
Whole Tale (RRID:SCR_017537) | project portal, data or information resource, 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 | 2026-07-28 09:44:37 | 1 | ||||||||
|
Center for Computational Biology at JHU Resource Report Resource Website 1+ mentions |
Center for Computational Biology at JHU (RRID:SCR_016680) | CCB at JHU | data or information resource, organization portal, portal | Center for Computational Biology as a joint research center in the McKusick-Nathans Institute of Genetic Medicine, spanning the School of Medicine, the Whiting School of Engineering, the Bloomberg School of Public Health, and the Krieger School of Arts & Sciences. Multidisciplinary center dedicated to research on genomics, genetics, DNA sequencing technology, and computational methods for DNA and RNA sequence analysis. | center, computational, biology, genomics, genetics, DNA, RNA, sequence, technology, analysis |
has parent organization: Johns Hopkins University; Maryland; USA is parent organization of: Centrifuge Classifier |
SCR_016680 | CCB at Johns Hopkins University, CCB at JHU, Center for Computational Biology at JHU, Center for Computational Biology at Johns Hopkins University | 2026-07-28 09:44:21 | 1 | |||||||||
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ReproNim: A Center for Reproducible Neuroimaging Computation Resource Report Resource Website 10+ mentions |
ReproNim: A Center for Reproducible Neuroimaging Computation (RRID:SCR_016001) | ReproNim | data or information resource, organization portal, portal | Center to help neuroimaging researchers to find and share data in FAIR fashion, to describe their data and analysis workflows in replicable fashion, to manage their computational resource options so that outcomes of neuroimaging research are more reproducible. | Neuroimaging, share, data, FAIR, analysis, manage, reproducible |
is related to: ABCD-ReproNim Course is related to: SVNTest is parent organization of: ReproIn: The ReproNim image input management system (featuring DataLad) |
NIBIB P41 EB019936 | Restricted | SCR_016005 | http://repronim.org | SCR_016001 | 2026-07-28 09:44:02 | 12 | ||||||
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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 | 2026-07-28 09:44:43 | 38 |
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