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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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SEDFIT Resource Report Resource Website 10+ mentions |
SEDFIT (RRID:SCR_018365) | data analysis software, data processing software, software application, 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 | 2026-08-29 11:26:07 | 32 | ||||||||
|
Phyutility Resource Report Resource Website 10+ mentions |
Phyutility (RRID:SCR_018545) | data analysis software, data processing software, software application, 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 | 2026-08-29 11:26:09 | 46 | ||||||
|
PRISMA Resource Report Resource Website 1000+ mentions |
PRISMA (RRID:SCR_018721) | PRISMA | data or information resource, narrative resource, portal, standard specification | 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 | 2026-08-29 11:26:12 | 1593 | |||||||
|
ELDA Resource Report Resource Website 100+ mentions |
ELDA (RRID:SCR_018933) | analysis service resource, data analysis software, data processing software, production service resource, service resource, software application, software resource | 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 | 2026-08-29 11:26:15 | 463 | ||||||||
|
PROCHECK Resource Report Resource Website 100+ mentions |
PROCHECK (RRID:SCR_019043) | data analysis software, data processing software, software application, 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 | 2026-08-29 11:26:18 | 122 | |||||||||
|
igraph Resource Report Resource Website 100+ mentions |
igraph (RRID:SCR_019225) | data analysis software, data processing software, data visualization software, network analysis software, network graph visualization software, software application, software resource, software toolkit | 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 | 2026-08-29 11:26:20 | 432 | ||||||||
|
OpenClinica Resource Report Resource Website 10+ mentions |
OpenClinica (RRID:SCR_019223) | data acquisition software, data processing software, software application, 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 | 2026-08-29 11:25:59 | 46 | ||||||||
|
CalcuSyn Resource Report Resource Website 50+ mentions |
CalcuSyn (RRID:SCR_020251) | data analysis software, data processing software, software application, 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 | 2026-08-29 11:26:40 | 68 | |||||||||
|
CFX Manager Resource Report Resource Website 100+ mentions |
CFX Manager (RRID:SCR_017251) | data analysis software, data processing software, software application, software resource | Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | RT PCR, real time PCR, data, analysis, BioRad | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_017251 | CFX Manager software | 2026-08-29 11:25:58 | 492 | |||||||||
|
RNAstructure Resource Report Resource Website 50+ mentions |
RNAstructure (RRID:SCR_017216) | analysis service resource, data access protocol, production service resource, service resource, simulation software, software application, software resource, web service | Web server for RNA and DNA secondary structure prediction and analysis. Software package as RNA folding prediction program. | RNA, DNA, secondary, structure, prediction, analysis |
is listed by: SoftCite has parent organization: University of Rochester; New York; USA |
NIGMS R01 GM076485 | PMID:23620284 | Free, Freely available | SCR_017216 | 2026-08-29 11:25:30 | 58 | ||||||||
|
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 | 2026-08-29 11:25:33 | 10545 | ||||||||
|
FCS Express Resource Report Resource Website 500+ mentions |
FCS Express (RRID:SCR_016431) | data analysis software, data processing software, software application, 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 | 2026-08-29 11:25:44 | 518 | ||||||||||
|
BLASTClust Resource Report Resource Website 50+ mentions |
BLASTClust (RRID:SCR_016641) | data analysis software, data processing software, sequence analysis software, software application, software resource | 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 | 2026-08-29 11:25:19 | 94 | ||||||||||
|
CTFFIND Resource Report Resource Website 100+ mentions |
CTFFIND (RRID:SCR_016732) | CTFFIND | data analysis software, data processing software, software application, 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 | 2026-08-29 11:25:22 | 114 | ||||||||
|
EMAN Resource Report Resource Website 100+ mentions |
EMAN (RRID:SCR_016867) | EMAN | data processing software, image processing software, software application, 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 | 2026-08-29 11:25:52 | 107 | |||
|
Rhinoceros Resource Report Resource Website 100+ mentions |
Rhinoceros (RRID:SCR_014339) | simulation software, software application, software resource, standalone software | 3D modeling software used to create, edit, analyze, document, render, animate, and translate surfaces, solids, point clouds, and polygon meshes. It can also be used to analyze and manufacture a variety of products. | 3d, modeling software, standalone software | is listed by: SoftCite | Pay for product | SCR_014339 | Rhino | 2026-08-29 11:28:48 | 311 | |||||||||
|
STRUCTURE Resource Report Resource Website 1000+ mentions |
STRUCTURE (RRID:SCR_017637) | software resource, software toolkit | Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms. | Multi locus genotype data, investigate population structure, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: STRAT has parent organization: Stanford University; Stanford; California works with: Structure Harvester |
PMID:21564903 PMID:18784791 PMID:12930761 PMID:10835412 |
Free, Available for download, Freely available | SCR_021634, nlx_154662, SCR_002151, biotools:structure | https://bio.tools/structure, http://pritch.bsd.uchicago.edu/structure.html, | SCR_017637 | structure, Structure | 2026-08-29 11:28:48 | 4177 | ||||||
|
Argus Resource Report Resource Website 1+ mentions |
Argus (RRID:SCR_021585) | data or information resource, portal, project portal, software resource | Portal provides software tool for analysis and quantification of both single and socially interacting zebrafish. Software data extraction and analysis tool built in open source R language for tracking zebrafish behavior. | Analysis, quantification, socially interacting zebrafish, OpenBehavior |
is listed by: OpenBehavior is listed by: SoftCite is related to: Argus |
DOI:10.3758/s13428-018-1083-y | Free, Freely available | SCR_021619 | SCR_021585 | 2026-08-29 11:28:57 | 1 | ||||||||
|
GeneTools Resource Report Resource Website 100+ mentions |
GeneTools (RRID:SCR_022505) | data processing software, image analysis software, software application, software resource | Software package includes comprehensive tools to provide full range of analysis for applications including chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging and colony counting. | Synoptics Ltd., Syngene, chemiluminescence, chemifluorescence, fluorescence, colorimetric imaging, colony counting. | is listed by: SoftCite | Restricted | SCR_022505 | 2026-08-29 11:29:04 | 201 | ||||||||||
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CLC Main Workbench Resource Report Resource Website 10+ mentions |
CLC Main Workbench (RRID:SCR_000354) | CLC Main Workbench | software resource, software toolkit | A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management. | sequencing, analysis, cloning, data, management, molecular, gene, genome, dna, rna |
is listed by: OMICtools is listed by: SoftCite |
Restricted | OMICS_01813 | SCR_000354 | 2026-08-29 11:30:37 | 31 |
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