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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Ligprep Resource Report Resource Website 10+ mentions |
Ligprep (RRID:SCR_016746) | Ligprep | software resource, simulation software, software application | Software tool to correct and optimize the ligands by generating different protonation states, stereochemistry, tautomers, and ring conformations. Used to generate accurate, energy minimized 3D molecular structures. | correct, optimize, ligand, protonation, stereochemistry, tautomer, conformation, energy, minimized, 3D, moleular, structure |
is listed by: OMICtools is listed by: SoftCite has parent organization: Schrodinger works with: Glide works with: Phase |
Commercially available | SCR_016746 | LigPrep, LigandPreparation, Ligand preparation | 2026-02-14 02:03:19 | 48 | ||||||||
|
Epik Resource Report Resource Website 1+ mentions |
Epik (RRID:SCR_016745) | software resource, simulation software, software application | Software program for pKa prediction and protonation state generation for drug like molecules. | predict, pKa, value, chemical, structure, drug, profile, protonation, state, molecule, Schrodinger |
is listed by: OMICtools is listed by: SoftCite has parent organization: Schrodinger |
PMID:17899391 | Commercially available | SCR_016745 | 2026-02-14 02:03:09 | 5 | |||||||||
|
NetworkX Resource Report Resource Website 100+ mentions |
NetworkX (RRID:SCR_016864) | network analysis software, data processing software, data analysis software, software application, software resource | 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 | 2026-02-14 02:03:17 | 111 | |||||||||
|
BRASS Resource Report Resource Website 10+ mentions |
BRASS (RRID:SCR_017091) | data analysis software, software resource, data processing software, software application | Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements. | analysis, BAM, file, paired, end, sequencing, determine, rearrangement, breakpoint, assemble |
is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | SCR_017091 | 2026-02-14 02:03:14 | 42 | ||||||||||
|
Google Resource Report Resource Website 100+ mentions |
Google (RRID:SCR_017097) | commercial organization | American multinational technology company that specializes in internet related services and products, which include online advertising technologies, search engine, cloud computing, software, and hardware. Considered one of Big Four technology companies, alongside Amazon, Apple and Facebook. | technology, company, internet, service, product, search, engine, cloud, computing, software, hardware, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: SoftCite is parent organization of: golang |
grid.420451.6, Crossref funder ID: 100006785, ISNI, Wikidata: Q95, biotools:Google | https://ror.org/00njsd438 https://bio.tools/Google |
SCR_017097 | Google LLC | 2026-02-14 02:03:14 | 332 | ||||||||
|
Epi Info Resource Report Resource Website 10+ mentions |
Epi Info (RRID:SCR_021682) | data processing software, data analysis software, data analytics software, software toolkit, software application, software resource | Software suite of interoperable software tools designed for global community of public health practitioners and researchers. Provides easy data entry form and database construction, customized data entry experience, and data analysis with epidemiologic statistics, maps, and graphs for public health professionals who may lack information technology background.Statistical software for epidemiology developed by Centers for Disease Control and Prevention in Atlanta, Georgia. Available for Microsoft Windows, Android and iOS, along with web and cloud version. | Centers for Disease Control and Prevention, data analysis, epidemiologic statistics, maps, graphs, public health professionals tools | is listed by: SoftCite | Free, Available for download, Freely available | SCR_021682 | Epi Info TM, Epi Info™, Epi Info 6, Epi Info 7 | 2026-02-14 02:04:20 | 24 | |||||||||
|
Heidelberg Eye Explorer Resource Report Resource Website 10+ mentions |
Heidelberg Eye Explorer (RRID:SCR_022045) | data management software, software resource, software application | Platform that centralizes management of ophthalmic images. HEYEX interfaces with electronic medical record systems and third-party devices to allow exchange, storage, and dynamic review of diagnostic images. Heidelberg Engineering imaging products use Heidelberg Eye Explorer software platform and database to store patient information and images. | ophthalmic images management, Heidelberg Engineering imaging products, software to store patient information, software to store images | is listed by: SoftCite | Free, Available for download, Freely available | https://www.eyeoptics.dk//files/pdf/heidelberg/hrt_3_brochure_-_three_pearls_in_one_shell_english.pdf https://business-lounge.heidelbergengineering.com/us/en/products/heidelberg-eye-explorer/heyex-2/downloads/#downloads |
SCR_022045 | HEYEX 2, HEYEX | 2026-02-14 02:04:43 | 16 | ||||||||
|
MATLAB Resource Report Resource Website 10000+ mentions |
MATLAB (RRID:SCR_001622) | MATLAB | data processing software, software application, image processing software, software resource, programming language | Multi paradigm numerical computing environment and fourth generation programming language developed by MathWorks. Allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages, including C, C++, Java, Fortran and Python. Used to explore and visualize ideas and collaborate across disciplines including signal and image processing, communications, control systems, and computational finance. | computing, analyze, visualization, algorithm, plot, vector, matrix |
uses: Functional Network Connectivity (FNC) uses: MVGC Multivariate Granger Causality Matlab Toolbox uses: UltraMegaSort 2000 uses: Elastica2D uses: OSort uses: COMPASS is used by: Virtual Electrode Recording Tool for EXtracellular potentials (VERTEX) is used by: Orientation Distribution Function in Constant Solid Angle (CSA-ODF) is used by: NiiStat is used by: NeuroElf is used by: MRIcroS is used by: GraphVar: A toolbox for comprehensive graph analyses of functional brain connectivity is used by: GIMME is used by: GazeReader is used by: Efficient Permutation Testing is used by: APERTURE is used by: Tscratch is used by: PreSurgMapp is used by: SimTracker is used by: ICASSO is used by: TherMos is used by: Mixed Effect Model of Genetic-Set and Environment Interaction is used by: FMAToolbox is used by: BABAM is used by: Soma-Segmentation is used by: SpiSOP is used by: CHIPS is used by: GrowthToolbox is used by: RNAcompete is used by: MicrobeTracker is used by: Sound Analysis Pro is used by: Vocal Inventory Clustering Engine (VoICE) is used by: Automatic Analysis is used by: Measurement Control And Data Analysis Software is used by: Fluorescent Imaging Analysis Software FIMAS is used by: GEMB is used by: IronClust is used by: PAM is used by: calciumImagingAnalysis is used by: TractionsForAll is used by: DeePVP is used by: FieldTrip is used by: Protofilament Bending Models is used by: Toolkit for MIRA LAB Striatal Segmentation is used by: EvaluateMuscleTissueWithElastography is used by: Microscopy_tif_Channel_Quant_MATLAB is used by: CARNet TFA Function is listed by: SoftCite is related to: Spatio- Spectro- Temporal Receptive Field is related to: Extensible MATLAB Medical image Analysis is related to: MultiPhase-SEG is related to: An Open-Source MATLAB-to-Python Compiler is related to: Mastrave modelling library is related to: Libeep EEGLAB plugin is related to: The Bergen fMRI Toolbox Plugin for EEGLab is related to: Electrographic Seizure Analyzer is related to: BVA import/export EEGLAB plugin is related to: ROIs selection with a non-graphical user interface is related to: Reglo ICC control with Matlab is related to: QModeling is related to: MicroFilament Analyzer is related to: Letswave is related to: KiloSort is related to: Suite2P is related to: kCSD-Matlab is related to: nonparametricGGC_toolbox is related to: User Friendly Functional Connectivity - UF²C is related to: Frozen Noise is related to: Microscopy Image Browser is related to: MrDiffusion is related to: rsfMRI_fconn calculation is related to: SPM is related to: Colour maps for brain imaging is related to: Tools for NIfTI and ANALYZE image is related to: PESTO is related to: PPR-Meta is related to: NMF Toolbox is related to: SynapseLocator is related to: SBFSEM-tools is related to: Brain Gene Expression Analysis toolbox is related to: Neural Ideal is related to: Computer Vision System Toolbox is related to: LAN toolbox is related to: hMRI-toolbox is related to: Brainstorm is related to: auto_acpc_reorient is related to: SuperSegger is related to: MNE software is related to: Toolbox for Representational Similarity Analysis is related to: Sandwich Estimator Toolbox is related to: alpha helix coordinate frame simulation is related to: ZebEyeTrack is related to: PottersWheel is related to: Calliope calcium imaging processing package is related to: MVPA Light is related to: Amsterdam Decoding And Modeling is related to: Residue Iteration Decomposition is related to: ObjectFinder is related to: Deep Learning Toolbox is required by: OSort is required by: COMPASS is required by: MicrobeTracker is required by: Wave_clus is required by: Mass Univariate ERP Toolbox is required by: Linear Fascicle Evaluation is required by: PALM works with: CoSMoMVPA works with: Nexus works with: Empirical Gramian Framework works with: OriginPro works with: circular statistics works with: MRspa |
PMID:30609523 PMID:21934110 |
Restricted | nlx_153890 | SCR_001622 | matlab, MATLAB -The Language of Technical Computing, MATLAB, matrix laboratory | 2026-02-14 02:04:27 | 61711 | ||||||
|
ASPicDB Resource Report Resource Website 1+ mentions |
ASPicDB (RRID:SCR_002102) | ASPicDB | data or information resource, database | A database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation. | annotation, splicing pattern, gene, transcript, intron, protein, variant, alternative splicing, splicing, blast, exon, u2, u12, isoform |
is listed by: OMICtools is listed by: SoftCite has parent organization: University of Bari; Bari; Italy |
Normal, Cancer | PMID:21051348 PMID:18388144 |
Free, Freely available | OMICS_01882 | http://srv00.ibbe.cnr.it/ASPicDB/ | SCR_002102 | Alternative Splicing Prediction Data Base, ASPicDB - A Database tool for alternative splicing analysis | 2026-02-14 02:06:04 | 7 | ||||
|
SAM Resource Report Resource Website 100+ mentions |
SAM (RRID:SCR_010951) | software resource | Software for genomic expression data mining using a statistical technique for finding significant genes in a set of microarray experiments. | genomic expression, data mining, finding significant genes, microarray experiments, |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite is related to: pysam has parent organization: Stanford University; Stanford; California |
Commercial use requires license, Registration required | OMICS_01314, OMICS_00779, SCR_011888 | https://sources.debian.org/src/r-cran-samr/ | SCR_010951 | SAM: Significance Analysis of Microarrays, Significance Analysis of Microarrays | 2026-02-14 02:07:43 | 235 | |||||||
|
Design-Expert Resource Report Resource Website 10+ mentions |
Design-Expert (RRID:SCR_022671) | data analytics software, software resource, software application | Statistical software package from Stat-Ease Inc. to perform design of experiments. Offers comparative tests, screening, characterization, optimization, robust parameter design, mixture designs and combined designs. | Stat-Ease Inc., experiments design, comparative tests, screening, characterization, optimization, parameter design, mixture designs, combined designs | is listed by: SoftCite | Restricted | SCR_022671 | 2026-02-14 02:07:32 | 41 | ||||||||||
|
Treerecs Resource Report Resource Website 1+ mentions |
Treerecs (RRID:SCR_024497) | software resource, software application | Open source, species and gene tree reconciliation software. Software integrated phylogenetic tool, from sequences to reconciliations. Used to correct, rearrange and reroot gene trees with regard to given species tree. | species and gene tree reconciliation, integrated phylogenetic, from sequences to reconciliations, correct gene trees, rearrange gene trees, reroot gene trees, | is listed by: SoftCite | PMID:33085745 | Free, Available for download, Freely available | https://project.inria.fr/treerecs/ | SCR_024497 | 2026-02-14 02:07:25 | 1 | ||||||||
|
Evalue Resource Report Resource Website 10+ mentions |
Evalue (RRID:SCR_024506) | software resource, source code, web application | Web application as E-value calculator that compute E-values for variety of outcome measures, including risk ratios, odds ratios, rate ratios, risk differences, hazard ratios, and standardized mean differences. | E-value calculator, compute E-values for variety of outcome measures, | is listed by: SoftCite | PMID:29912013 | Free, Available for download, Freely available | https://github.com/mayamathur/evalue_package | SCR_024506 | 2026-02-14 02:07:16 | 14 | ||||||||
|
Web of Science Resource Report Resource Website 10+ mentions |
Web of Science (RRID:SCR_022706) | data or information resource, database | Database of bibliographic citations of multidisciplinary areas that covers various journals of medical, scientific, and social sciences including humanities.Publisher independent global citation database. | Clarivate, publisher independent, global citation database, bibliographic citations of multidisciplinary areas, various journals | is listed by: SoftCite | Free | SCR_022706 | Web of Knowledge | 2026-02-14 02:06:50 | 18 | |||||||||
|
CASAVA Resource Report Resource Website 1000+ mentions |
CASAVA (RRID:SCR_001802) | CASAVA | software resource, software application | Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting | gene, genetic, genomic, linux |
is listed by: OMICtools is listed by: Genetic Analysis Software is listed by: SoftCite |
Free, Available for download, Freely available | nlx_154257, OMICS_01123 | http://www.illumina.com/software/genome_analyzer_software.ilmn | SCR_001802 | Consensus Assessment of Sequence And VAriation | 2026-02-14 02:06:54 | 1899 | ||||||
|
qBasePLUS Resource Report Resource Website 100+ mentions |
qBasePLUS (RRID:SCR_003370) | qbase+ | software resource, commercial organization | Software program for quantitative PCR (qPCR) data analysis based on geNorm and qBase technology. | real-time quantitative pcr |
is listed by: OMICtools is listed by: SoftCite is related to: geNORM has parent organization: Biogazelle |
PMID:17291332 | Free, Available for download, Freely available | OMICS_02320 | https://biogazelle-qbaseplus.software.informer.com/2.0/ | http://medgen.ugent.be/qbase/ | SCR_003370 | 2026-02-14 02:07:20 | 343 | |||||
|
Picard Resource Report Resource Website 10000+ mentions Rating or validation data |
Picard (RRID:SCR_006525) | software resource, source code, software toolkit | Java toolset for working with next generation sequencing data in the BAM format. | next generation sequencing, java, bam |
is listed by: OMICtools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge has parent organization: Broad Institute is required by: SL-quant |
Available for download, Free | OMICS_01066 | http://sourceforge.net/projects/picard/ https://github.com/broadinstitute/picard https://sources.debian.org/src/picard-tools/ |
SCR_006525 | 2026-02-14 02:07:56 | 14139 | ||||||||
|
GENIE Resource Report Resource Website 100+ mentions |
GENIE (RRID:SCR_009197) | GENIE | software resource, software application | Software application that performs tests of association and transmission disequilibrium (TDT) between genetic markers and traits in studies of arbitrarily-sized families and/or independent individuals using Monte Carlo testing. For dichotomous traits, basic genotype-based or allele-based Chi-square statistics, OR, and a Chi-square trend statistic with user-defined weights, TDT, sib-TDT, combined-TDT are included. For quantitative outcomes, a difference in means test, ANOVA and QTDT are offered. Flexible haplotype testing and meta analysis across multiple centers are available. An automated haplotype building module, hapConstructor, is also offered that data mines multi-locus data for association signals. The Monte Carlo empirical significance assessment accounts for all relatedness between individuals for all tests. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, java 1.6, web-based |
is listed by: Genetic Analysis Software is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154344 | http://bioinformatics.med.utah.edu/Genie/index.html | SCR_009197 | PEDGENIE, HAPMC | 2026-02-14 02:07:01 | 361 | ||||||
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PROFILER Resource Report Resource Website 1000+ mentions |
PROFILER (RRID:SCR_009339) | PROFILER | software resource, software application | A flexible software tool to generate the probability distribution of joint multilocus genotypes defined by sets of individuals within the pedigree and sets of markers within the framework map. (entry from Genetic Analysis Software), THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | gene, genetic, genomic, linux, unix, solaris |
is listed by: Genetic Analysis Software is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154552 | SCR_009339 | 2026-02-14 02:07:13 | 1294 | ||||||||
|
Adobe Illustrator Resource Report Resource Website 10000+ mentions |
Adobe Illustrator (RRID:SCR_010279) | Illustrator CC | software resource, software toolkit, software application | Vector graphics software to create digital graphics, illustrations, and typography for several types of media: print, web, interactive, video, and mobile. | vector graphics, graphics, illustration, typography, adobe, software |
uses: National Gene Vector Laboratories is listed by: SoftCite is related to: Adobe Illustrator |
SCR_014198, nlx_157287 | http://www.adobe.com/products/cs6.html | SCR_010279 | Illustrator CC, Adobe Illustrator CS5, Adobe Illustrator CS6 | 2026-02-14 02:07:09 | 12706 |
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