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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Cistrome Resource Report Resource Website 10+ mentions |
Cistrome (RRID:SCR_000242) | data access protocol, software resource, web service | Web based integrative platform for transcriptional regulation studies. | Transcriptional, regulation, Chip, data, analysis, genome, gene, expression, motif, mining, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Galaxy has parent organization: Harvard University; Cambridge; United States |
Dana-Farber Cancer Institute High Tech and Campaign Technology Fund ; National Basic Research Program of China ; NHGRI HG004069; NIDDK DK062434; NIDDK DK074967 |
PMID:21859476 | Free, Freely available | SCR_017663, biotools:cistrome, OMICS_02173 | http://cistrome.org/ap/root, https://bio.tools/cistrome | SCR_000242 | Galaxy Cistrome | 2026-09-19 12:49:18 | 17 | |||||
|
miRanalyzer Resource Report Resource Website 1+ mentions |
miRanalyzer (RRID:SCR_000163) | software resource, web application | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. A microRNA detection and analysis tool for next-generation sequencing experiments. The program uses a minimum match length of 17bp starting at the first base of the read. The maximum read length is set to 28bp. Reads with more than 5 matches to the genome are discarded, and if a read matches to more than 5 transcripts or Rfam entries it will be removed. | mirna, microrna, next gen sequencing, analysis, next generation, next gen, detection tool, analysis tool | is listed by: OMICtools | PMID:21515631 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00361 | SCR_000163 | 2026-09-19 12:49:17 | 8 | ||||||||
|
Lasergene's SeqMan Pro Resource Report Resource Website 1+ mentions |
Lasergene's SeqMan Pro (RRID:SCR_000283) | data analysis software, data processing software, data visualization software, software application, software resource | Software for analysis and DNA sequence assembly of Sanger data. It also provides visualizations and analysis of next-gen projects assembled by SeqMan NGen. | dna, sequence, analysis, sanger, snp discovery, data visualization |
is listed by: OMICtools works with: GenVision |
Restricted | OMICS_01810 | SCR_000283 | Lasergenes SeqMan Pro, SeqMan Pro, SeqMan Pro - Software for Contig Assembly and Analysis Including SNP Discovery Coverage Evaluation and Project Annotation, DANSEUR Lasergenes SeqMan Pro | 2026-09-19 12:49:20 | 5 | ||||||||
|
F2DockClient Resource Report Resource Website 1+ mentions |
F2DockClient (RRID:SCR_000185) | F2DockClient | software resource | A collection of user interfaces packaged into TexMol that allows a user to interactively submit protein-protein docking jobs to a remote computing cluster, monitor the status of the jobs and retrieve and visually display/compare the results. | user interface, protein-protein docking, computing cluster, analysis, | is listed by: OMICtools | National Science Foundation ; National Institutes of Health |
PMID:23483883 | Free, Available for download, Freely available | OMICS_01599 | SCR_000185 | 2026-09-19 12:49:17 | 1 | ||||||
|
FlexX Resource Report Resource Website 1+ mentions |
FlexX (RRID:SCR_000186) | FlexX | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. A software with two main applications: predicting the binding mode of three-dimensional proteins and virtual high-throughput screening (vHTS) which allows screening of compounds at rapid speeds. | protein binding, analysis, ligand, prediction, compounds, screening, protein-ligand docking, | is listed by: OMICtools | PMID:15382244 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01600 | SCR_000186 | 2026-09-19 12:49:17 | 5 | |||||||
|
MACS Resource Report Resource Website 1000+ mentions |
MACS (RRID:SCR_013291) | MACS | data analysis software, data processing software, software application, software resource | Software Python package for identifying transcript factor binding sites. Used to evaluate significance of enriched ChIP regions. Improves spatial resolution of binding sites through combining information of both sequencing tag position and orientation. Can be used for ChIP-Seq data alone, or with control sample with increase of specificity. | identify, transcript, factor, binding, site, model, based, analysis, CHIP Seq, short, read, sequencer, protein, DNA, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Dana-Farber Cancer Institute |
NHGRI HG004069; NHGRI HG004270; NIDDK DK074967 |
PMID:18798982 DOI:10.1186/gb-2008-9-9-r137 |
Free, Available for download, Freely available | OMICS_00446, biotools:macs | https://bio.tools/macs, https://sources.debian.org/src/macs/ | SCR_013291 | MACS - Model-based Analysis for ChIP-Seq, Model-based Analysis for ChIP-Seq, MACS2 | 2026-09-19 12:52:40 | 1418 | ||||
|
DOLOP: A Database of Bacterial Lipoproteins Resource Report Resource Website 10+ mentions |
DOLOP: A Database of Bacterial Lipoproteins (RRID:SCR_013487) | data or information resource, data repository, database, service resource, storage service resource | DOLOP is an exclusive knowledge base for bacterial lipoproteins by processing information from 510 entries to provide a list of 199 distinct lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins from 43 completed bacterial genomes along with interactive information exchange facility. This website along will have additional information on the biosynthetic pathway, supplementary material and other related figures. DOLOP also contains information and links to molecular details for about 278 distinct lipoproteins and predicted lipoproteins from 234 completely sequenced bacterial genomes. Additionally, the website features a tool that applies a predictive algorithm to identify the presence or absence of the lipoprotein signal sequence in a user-given sequence. The experimentally verified lipoproteins have been classified into different functional classes and more importantly functional domain assignments using hidden Markov models from the SUPERFAMILY database that have been provided for the predicted lipoproteins. Other features include: primary sequence analysis, signal sequence analysis, and search facility and information exchange facility to allow researchers to exchange results on newly characterized lipoproteins. | figure, functional, algorithm, analysis, bacterial, biosynthetic, classification, genome, lipid, lipoprotein, modification, molecular, molecule, pathogenesis, predictive, primary, prokaryote, query, sequence, signal | has parent organization: University of Cambridge; Cambridge; United Kingdom | nif-0000-21124 | SCR_013487 | DOLOP | 2026-09-19 12:52:42 | 16 | |||||||||
|
Extensible MATLAB Medical image Analysis Resource Report Resource Website 1+ mentions |
Extensible MATLAB Medical image Analysis (RRID:SCR_013499) | data processing software, data visualization software, software application, software resource, software toolkit | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. EMMA (Extensible MATLAB Medical image Analysis) is a toolkit designed to ease the use of MATLAB in the analysis of medical imaging data. It provides functions for reading and writing MINC files, viewing images, performing ROI operations, and performing several popular analyses. Also, there are toolkits for performing kinetic analysis of dynamic PET rCBF (regional cerebral blood flow) and FDG data. The goal for this site is to provide a centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools that are of use to the general community. | analysis, matlab, medical, neurological, tool, image, toolkit |
is listed by: Internet Analysis Tools Registry is related to: MATLAB is related to: MINC |
Human Brain Project | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-33081 | SCR_013499 | MINC-EMMA, EMMA | 2026-09-19 12:52:43 | 7 | |||||||
|
Image Studio Lite Resource Report Resource Website 100+ mentions |
Image Studio Lite (RRID:SCR_013715) | data analysis software, data processing software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 28,2023. Software application which can analyze basic Western blot data and export them for use in spreadsheet programs. Users can create standardized or custom lab reports and can share them with colleagues. Image Studio Lite has been discontinued and replaced with Empiria Studio Software. | Li-COR, Odyssey, infrared, immunoblot, western blot, analysis | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014211 | SCR_013715 | Image Studio Lite version 3.1, LICOR Image Studio Lite Software, LI-COR Image Studio Lite Software, Image Studio Lite Software | 2026-09-19 12:52:47 | 273 | |||||||||
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HED Tags Resource Report Resource Website 1+ mentions |
HED Tags (RRID:SCR_014074) | HED | data or information resource, narrative resource, standard specification | Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging. | Data, structure, standard, EEG, brain, imaging, comma, separated, path, string, analysis, MEG, fNIRS, multimodal, ECG, EMG, GSR, behavioral, BRAIN Initiative |
is used by: NIMH Data Archive is used by: HeadIT is used by: OpenNeuro is recommended by: BRAIN Initiative has parent organization: University of California at San Diego; California; USA |
Army Research Laboratory Cooperative Agreement ; NIMH R01MH084819; NINDS R01 NS047293; Swartz Foundation |
PMID:27799907 | Free, Freely available | SCR_017630 | SCR_014074 | Hierarchical Event Descriptor Tags, Hierarchical Event Descriptor, HED, HED tags | 2026-09-19 12:52:51 | 8 | |||||
|
Skyline Resource Report Resource Website 1000+ mentions |
Skyline (RRID:SCR_014080) | data analysis software, data processing software, software application, software resource | 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; NCRR P41 RR011823; NHLBI R01 HL082747; NIA P30 AG013280; NIDDK R01 DK069386 |
PMID:20147306 | Free, Available for download, Freely available | SCR_014080 | 2026-09-19 12:52:51 | 3040 | ||||||||
|
Origin Resource Report Resource Website 10000+ mentions |
Origin (RRID:SCR_014212) | data analysis software, data processing software, data visualization software, software application, software resource | 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 | 2026-09-19 12:52:53 | 13985 | |||||||
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Genboree Workbench Resource Report Resource Website |
Genboree Workbench (RRID:SCR_011864) | Genboree | service resource | Service where users are able to upload and store data, access bioinformatics tools, and perform analyses. | metagenome, visualization, genome, transcriptiome, cistrome, epigenome, analysis, rna-seq, chip-seq |
is listed by: OMICtools has parent organization: Baylor University; Texas; USA |
Free for academic use | OMICS_01142 | SCR_011864 | 2026-09-19 12:52:19 | 0 | ||||||||
|
Princeton High Throughput Sequencing and Microarray Facility Resource Report Resource Website |
Princeton High Throughput Sequencing and Microarray Facility (RRID:SCR_012619) | Princeton High Throughput Sequencing and Microarray Facility, High Throughput Sequencing and Microarray Facility | access service resource, analysis service resource, core facility, data analysis service, production service resource, service resource | Core facility provides researchers with access to high-throughput sequencing technologies. The staff provide consultation on experimental design, library preparation, and data analysis. The Sequencing Core Facility works closely with Bioinformatics staff in the Center for Quantitative Biology to provide researchers with computing power and consulting services to analyze sequencing data. | sequence, microarray, data analysis, analysis, consulting, |
is listed by: ScienceExchange is related to: Princeton University Labs and Facilities has parent organization: Princeton University; New Jersey; USA |
Available to External User | SciEx_567 | SCR_012619 | High Throughput Sequencing, Microarray, Princeton University, Facility | 2026-09-19 12:52:31 | 0 | |||||||
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The Immunology Database and Analysis Portal (ImmPort) Resource Report Resource Website 1000+ mentions |
The Immunology Database and Analysis Portal (ImmPort) (RRID:SCR_012804) | ImmPort | controlled vocabulary, data or information resource, data repository, database, disease-related portal, ontology, portal, service resource, storage service resource, topical portal | Data sharing repository of clinical trials, associated mechanistic studies, and other basic and applied immunology research programs. Platform to store, analyze, and exchange datasets for immune mediated diseases. Data supplied by NIAID/DAIT funded investigators and genomic, proteomic, and other data relevant to research of these programs extracted from public databases. Provides data analysis tools and immunology focused ontology to advance research in basic and clinical immunology. | immunology, basic, clinical, data, share, store, analyze, exchange, dataset, immune, mediated, disease, analysis, tool, FASEB list |
is recommended by: National Library of Medicine is recommended by: NIDDK Information Network (dkNET) is recommended by: NIDDK - National Institute of Diabetes and Digestive and Kidney Diseases is listed by: NIDDK Research Resources is affiliated with: Cytokine Registry is related to: MetaCyto is related to: The 10000 Immunomes is related to: NIAID |
Immune mediated disease | DAIT ; NIAID ; NIAID HHSN266200400076C; NIAID HHSN272201200028C; NIH |
PMID:24791905 | nlx_152691, r3d100012529 | http://www.immport.org/immport-open/public/home/home, http://www.immport.org/ | http://www.immport.org | SCR_012804 | Immunology Data and Analysis Portal, ImmPort system, ImmPort, Immunology Database and Analysis Portal | 2026-09-19 12:52:32 | 1383 | |||
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Maple Resource Report Resource Website 100+ mentions |
Maple (RRID:SCR_014449) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-19 12:52:57 | 155 | |||||||||||
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Wolfram Mathematica Resource Report Resource Website 500+ mentions |
Wolfram Mathematica (RRID:SCR_014448) | data analytics software, data processing software, data storage software, data visualization software, software application, software resource | 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 | 2026-09-19 12:52:57 | 511 | |||||||||||
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VolView Resource Report Resource Website 50+ mentions |
VolView (RRID:SCR_014569) | 3d spatial image, data or information resource, data processing software, image, image analysis software, image processing software, software application, software resource | 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 | 2026-09-19 12:52:58 | 62 | ||||||||||
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FactoMineR Resource Report Resource Website 1000+ mentions |
FactoMineR (RRID:SCR_014602) | data analysis software, data processing software, software application, software resource | 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 | 2026-09-19 12:52:59 | 2608 | |||||||||
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FastQC Resource Report Resource Website 10000+ mentions Rating or validation data |
FastQC (RRID:SCR_014583) | data analysis software, data management software, data processing software, software application, software resource | 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 | 2026-09-19 12:52:59 | 19827 |
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