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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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MRIcron Resource Report Resource Website 1000+ mentions |
MRIcron (RRID:SCR_002403) | MRIcron | software application, data visualization software, data processing software, software resource | Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron. | NIfTI, format, image, viewer, exporting, brain, image, processing, data, bio.tools |
is used by: XFSL: An FSL toolbox is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Biositemaps is listed by: neurodebian is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Colour maps for brain imaging has parent organization: University of South Carolina; South Carolina; USA |
PMID:17583985 PMID:11568431 |
BSD License | biotools:MRIcron, nif-0000-00122 | https://sources.debian.org/src/mricron/ http://www.mccauslandcenter.sc.edu/mricro/ http://www.nitrc.org/projects/mricron http://neuro.debian.net/pkgs/mricron.html https://bio.tools/MRIcron |
SCR_002403 | mricron - magnetic resonance image conversion viewing and analysis | 2026-02-15 09:18:18 | 2194 | |||||
|
BLASTP Resource Report Resource Website 100+ mentions |
BLASTP (RRID:SCR_001010) | service resource, analysis service resource, data analysis service, production service resource | Data analysis service whose programs search protein databases using a protein query. The algorithms used include blastp, psi-blast, phi-blast, and delta-blast. | blast, basic local alignment search tool, protein alignment, protein blast, data analysis service, protein |
is used by: Open Reading Frame Finder is listed by: OMICtools is listed by: SoftCite has parent organization: NCBI |
Freely available, Acknowledgement requested | OMICS_00991 | SCR_001010 | blastp suite, Standard Protein BLAST | 2026-02-15 09:18:01 | 286 | ||||||||
|
Primer-BLAST Resource Report Resource Website 5000+ mentions |
Primer-BLAST (RRID:SCR_003095) | Primer-BLAST | service resource, analysis service resource, data analysis service, production service resource | A tool to design target-specific primers for polymerase chain reaction (PCR). It uses Primer3 to design PCR primers and then uses BLAST and global alignment algorithm to screen primers against user-selected database in order to avoid primer pairs (all combinations including forward-reverse primer pair, forward-forward as well as reverse-reverse pairs) that can cause non-specific amplifications. | primer, blast, pcr target, polymerase chain reaction, primer design |
is listed by: OMICtools is listed by: SoftCite is related to: Primer3 has parent organization: NCBI |
PMID:22708584 | Free, Freely available | OMICS_02343 | SCR_003095 | 2026-02-15 09:18:26 | 5498 | |||||||
|
MutationAssessor Resource Report Resource Website 500+ mentions |
MutationAssessor (RRID:SCR_005762) | mutationassessor.org | service resource, analysis service resource, data analysis service, production service resource | A web server that predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or nonsynonymous polymorphisms. The functional impact is assessed based on evolutionary conservation of the affected amino acid in protein homologs. The method has been validated on a large set (51k) of disease associated (OMIM) and polymorphic variants., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | cancer, protein, mutation, function, amino-acid, substitution |
is listed by: OMICtools is listed by: SoftCite |
PMID:21727090 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00134, nlx_149228 | SCR_005762 | MutationAssessor - functional impact of protein mutations, MutationAssessor - functional impact of mutations, mutationassessor.org - functional impact of protein mutations | 2026-02-15 09:19:03 | 669 | ||||||
|
AMBER Resource Report Resource Website 1000+ mentions |
AMBER (RRID:SCR_016151) | AMBER | software application, data visualization software, data processing software, software resource, software toolkit, data analysis software | Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. | binning, metagenomics, benchmarking, biobox, evaluation, comparison, reconstruction, metric, |
is used by: CHARMM-GUI is listed by: SoftCite |
DOI:10.1101/239582 | Free, Available for download | SCR_016151 | AMBER: Assessment of Metagenome BinnERs | 2026-02-15 09:21:48 | 2204 | |||||||
|
FCS Express Resource Report Resource Website 100+ mentions |
FCS Express (RRID:SCR_016431) | software application, data processing software, data analysis software, software resource | Software tool for flow and image cytometry data analysis by De Novo Software company. | flow, image, analysis, data, cytometry, De Novo Software, research, clinical, laboratory | is listed by: SoftCite | Commercially available, Tutorial available | SCR_016431 | 2026-02-15 09:21:52 | 488 | ||||||||||
|
EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | software application, image processing software, data processing software, software resource | Software suite for processing data from transmission electron microscopes. Used in supercomputing facilities as a test application for large-scale computing. Used for single particle reconstruction, helical reconstruction, 2-D crystallography and whole-cell tomography. | image, processing, data, transmission, electron, microscope, single, particle, reconstruction, helical, 2D, whole, cell, tomography, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite |
NIH | PMID:16859925 | Free, Available for download, Freely available | biotools:eman | https://bio.tools/eman | https://blake.bcm.edu/emanwiki/EMAN1 | SCR_016867 | EMAN1, EMAN2 | 2026-02-15 09:21:55 | 106 | |||
|
BLASTClust Resource Report Resource Website 50+ mentions |
BLASTClust (RRID:SCR_016641) | software application, sequence analysis software, data processing software, software resource, data analysis software | Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets. | cluster, protein, nucleotide, sequence, pairwise, match, sequence |
is listed by: SoftCite has parent organization: NCBI works with: NCBI BLAST |
Free, Freely available | SCR_016641 | 2026-02-15 09:21:46 | 88 | ||||||||||
|
CTFFIND Resource Report Resource Website 100+ mentions |
CTFFIND (RRID:SCR_016732) | CTFFIND | software application, data processing software, data analysis software, software resource | Software tool for finding CTFs of electron micrographs. Program used for the estimation of objective lens defocus parameters from transmission electron micrographs. The program CTFFIND3 is an updated version of the program CTFFIND2. For micrographs collected on photographic film and scanned in use CTFFIND 3. For images from CCDs or direct detectors use CTFFIND 4. |
is listed by: SoftCite is related to: Janelia Research has parent organization: MRC Laboratory of Molecular Biology |
MRC | PMID:26278980 | SCR_016732 | CTFFinding, CTFFIND4, CTFFIND2, Contrast Transfer Function Finding, Contrast Transfer FunctionFinding, CTFFIND 3 | 2026-02-15 09:21:48 | 109 | ||||||||
|
SEDFIT Resource Report Resource Website 10+ mentions |
SEDFIT (RRID:SCR_018365) | software application, data processing software, data analysis software, software resource | Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly. | Analytical ultracentrifugation, biophysical analysis, macromolecular assembly, data, analysis, National Institute of Biomedical Imaging and Bioengineering | is listed by: SoftCite | NIH | Free, Available for download, Freely available | SCR_018365 | SEDFIT version 14.7g | 2026-02-15 09:22:21 | 25 | ||||||||
|
PRISMA Resource Report Resource Website 1000+ mentions |
PRISMA (RRID:SCR_018721) | PRISMA | data or information resource, narrative resource, standard specification, portal | Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions. | MDAR, standard, report standard, reporting reviews, randomized trial, evaluating randomized trial, reporting systematic review, intervention evaluation, meta analysis | is listed by: SoftCite | Ottawa Hospital Research Institute ; University of Oxford |
Free, Freely available | SCR_018721 | Preferred Reporting Items for Systematic Reviews and Meta-Analyses | 2026-02-15 09:22:16 | 1069 | |||||||
|
Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | software application, data processing software, data analysis software, software resource | Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI. | Data matrice analysis, data matrice modification, phyloinformatics, phylogenetic tree, alignment, molecular data manipulation, data analysis |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite is related to: NCBI |
NSF Cyberinfrastructure for Phylogenetic Research EF 0331654 | PMID:18227120 | Free, Freely available | OMICS_21687 | https://sources.debian.org/src/phyutility/ | SCR_018545 | 2026-02-15 09:22:16 | 42 | ||||||
|
ELDA Resource Report Resource Website 100+ mentions |
ELDA (RRID:SCR_018933) | software application, data processing software, software resource, service resource, production service resource, analysis service resource, data analysis software | Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly. | Limiting dilution analysis, stem cell assay, data set confidence intervals, single hit hypothesis, adequacy test, frequency differences test | is listed by: SoftCite | PMID:19567251 | Free, Freely available | SCR_018933 | Extreme Limiting Dilution Analysis | 2026-02-15 09:22:25 | 385 | ||||||||
|
PROCHECK Resource Report Resource Website 50+ mentions |
PROCHECK (RRID:SCR_019043) | software application, data processing software, data analysis software, software resource | Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR. | Stereochemical quality, protein structure, plot, residue listing, protein, assessing protein quality, | is listed by: SoftCite | DOI:10.1107/S0021889892009944 | Free, Available for download | SCR_019043 | 2026-02-15 09:22:21 | 75 | |||||||||
|
igraph Resource Report Resource Website 100+ mentions |
igraph (RRID:SCR_019225) | software application, data visualization software, data processing software, software resource, network graph visualization software, network analysis software, software toolkit, data analysis software | Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus. | Graphs analysis, network analysis, generating graph function, graph visualization |
is listed by: CRAN is listed by: SoftCite is related to: igraph for R |
Free, Available for download, Freely available | https://igraph.org/ https://github.com/igraph/igraph/releases/tag/0.8.4 |
SCR_019225 | igraph 0.8.4, igraph 1.2.6 | 2026-02-15 09:22:21 | 354 | ||||||||
|
OpenClinica Resource Report Resource Website 10+ mentions |
OpenClinica (RRID:SCR_019223) | software application, data processing software, data acquisition software, software resource | Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system. | Clinical trial, data management system, clinical trial management system, clinical data, clinical data management | is listed by: SoftCite | PMID:21893916 | Restricted | https://www.openclinica.com/community-edition-open-source-edc/ | SCR_019223 | 2026-02-15 09:22:28 | 35 | ||||||||
|
CalcuSyn Resource Report Resource Website 50+ mentions |
CalcuSyn (RRID:SCR_020251) | software application, data processing software, data analysis software, software resource | Software tool for drug mixtures study and establishing efficacy. Dose effect analyzer of combined drugs. Able to quantify synergism and inhibition. CalcuSyn Version 2.0 has Undo and Redo tools. | Biosoft, drug mixtures study, drug efficacy, dose effect, quantify synergism, quantify inhibition | is listed by: SoftCite | Restricted | SCR_020251 | CalcuSyn Version 2.0 | 2026-02-15 09:21:53 | 57 | |||||||||
|
Flowlogic Resource Report Resource Website 50+ mentions |
Flowlogic (RRID:SCR_020942) | software application, data processing software, data analysis software, software resource | Software tool for flow cytometry data analysis by Miltenyi Biotec. | Flow cytometry data, data analysis, flow cytometry, Miltenyi Biotec | is listed by: SoftCite | Restricted | SCR_020942 | Flowlogic TM Software, Flowlogic Software | 2026-02-15 09:22:27 | 74 | |||||||||
|
BoxPlotR Resource Report Resource Website 100+ mentions |
BoxPlotR (RRID:SCR_015629) | software application, data visualization software, data processing software, software resource, web application | Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox. | Box plot generation, customized box plot, data, plot, analysis |
is listed by: SoftCite is related to: PlotsOfData is related to: vioplot |
Wellcome Trust ; WTCCB ; ERC ; Genome Québec International Recruitment Award |
PMID:24481215 | Free, Available for download, Freely available | SCR_018327 | https://github.com/VizWizard/BoxPlotR.shiny | SCR_015629 | 2026-02-15 09:20:56 | 360 | ||||||
|
Phobius Resource Report Resource Website 100+ mentions |
Phobius (RRID:SCR_015643) | software resource, data access protocol, web service, service resource, production service resource, analysis service resource | Web application for combined transmembrane topology and signal peptide prediction. Used for whole genome annotation of signal peptides and transmembrane regions. Predictor is based on hidden Markov model (HMM) that models different sequence regions of signal peptide and different regions of transmembrane protein in series of interconnected states. | Signal peptide prediction, whole genome annotation, transmembrane region, protein prediction, transmembrane topology, signal peptide, fasta, hidden markov model | is listed by: SoftCite | PMID:15111065 PMID:30976793 |
Freely Available, Free, Available for download | SCR_018767 | http://phobius.binf.ku.dk/ https://www.ebi.ac.uk/Tools/pfa/phobius/ |
SCR_015643 | PHOBIUS | 2026-02-15 09:21:22 | 498 |
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