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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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ATSAS Resource Report Resource Website 1000+ mentions |
ATSAS (RRID:SCR_015648) | data processing software, software application, software resource, software toolkit | Software toolkit for small-angle scattering data analysis from biological macromolecules. | macromolecule, small-angle scattering, ab initio method, rigid body modeling, pbd oriented tool, mixture, flexible system |
is listed by: SoftCite is related to: DAMMIF |
PMID:28808438 | SCR_015648 | Data Analysis Software ATSAS | 2026-08-29 11:28:44 | 1377 | |||||||||
|
Phenix.refine Resource Report Resource Website 10+ mentions |
Phenix.refine (RRID:SCR_016736) | Phenix.refine | data processing software, software application, software resource | Software tool for a general purpose crystallographic structure refinement within the PHENIX package. Serves as a critical component in automated model building, final structure refinement, structure validation and deposition to the wwPDB. | crystallographic, structure, refinement, Phenix, model, building, validation |
is listed by: SoftCite is provided by: Phenix |
NIGMS GM063210; US Department of Energy |
PMID:22505256 | Free, Available for download for non profit, For profit access PHENIX through a Consortium agreement, Tutorial available, Acknowledgement requested | SCR_016736 | Python-based Hierarchical ENvironment for Integrated Xtallography.refine, Phenix.refine, Phenix | 2026-08-29 11:28:51 | 39 | ||||||
|
HALO Resource Report Resource Website 100+ mentions |
HALO (RRID:SCR_018350) | HALO | data processing software, image analysis software, software application, software resource | Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology. | Image analysis platform, digital pathology, quantitative tissue analysis, image, analysis, tissue | is listed by: SoftCite | Restricted | SCR_018350 | Indica Labs HALO software | 2026-08-29 11:28:49 | 108 | ||||||||
|
LaCyTools Resource Report Resource Website 10+ mentions |
LaCyTools (RRID:SCR_024525) | software resource, software toolkit | Software high throughput data extraction package for LC-MS data.Targeted Liquid Chromatography-Mass Spectrometry data processing package for relative quantitation of glycopeptides. | Targeted Liquid Chromatography, Mass Spectrometry Data Processing, relative quantitation of glycopeptides, | is listed by: SoftCite | PMID:27267458 | Free, Available for download, Freely available | SCR_024525 | 2026-08-29 11:29:07 | 26 | |||||||||
|
GOplot Resource Report Resource Website 100+ mentions |
GOplot (RRID:SCR_024419) | software resource, software toolkit | Software R package for visually combining expression data with functional analysis. | visually combining expression data with functional analysis, | is listed by: SoftCite | PMID:25964631 | Free, Available for download, Freely available | https://github.com/wencke/wencke.github.io | SCR_024419 | R GOplot | 2026-08-29 11:29:06 | 415 | |||||||
|
geepack Resource Report Resource Website 1+ mentions |
geepack (RRID:SCR_024510) | software resource, software toolkit | Software R package implements generalized estimating equations for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. Can handle clustered categorical responses. Used for fitting marginal generalized linear models to clustered data. | generalized estimating equations, fitting marginal generalized linear models to clustered data, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024510 | generalized estimating equations pack | 2026-08-29 11:29:06 | 3 | |||||||||
|
DAGitty Resource Report Resource Website 10+ mentions |
DAGitty (RRID:SCR_024509) | software resource, software toolkit | Software R package provides access to all of the capabilities of DAGitty web application for drawing and analysing Directed Acyclic Graphs within the R platform for statistical computing. Used for graphical analysis of structural causal models. | graphical analysis of structural causal models, drawing and analysing Directed Acyclic Graphs, | is listed by: SoftCite | PMID:28089956 | Free, Available for download, Freely available | https://github.com/jtextor/dagitty | SCR_024509 | 2026-08-29 11:29:12 | 25 | ||||||||
|
FastMulRFS Resource Report Resource Website 1+ mentions |
FastMulRFS (RRID:SCR_024505) | software resource, software toolkit | Software pipeline for estimating species trees from multi copy gene trees. | estimating species trees, multi copy gene trees, | is listed by: SoftCite | PMID:32657396 | Free, Available for download, Freely available | SCR_024505 | 2026-08-29 11:29:06 | 1 | |||||||||
|
NOTUNG Resource Report Resource Website 1+ mentions |
NOTUNG (RRID:SCR_024484) | software resource, software toolkit | Software package to facilitate large scale analysis, using both rooted and unrooted trees.Used for dating gene duplications and optimizing gene family trees.Used for inferring duplication dates from gene trees automatically and can also be used as exploratory analysis tool for evaluating alternative hypotheses. | inferring duplication dates, large scale analysis, dating gene duplications, optimizing gene family trees, | is listed by: SoftCite | PMID:11108472 | Free, Available for download, Freely available | SCR_024484 | Notung 2.9 | 2026-08-29 11:29:12 | 9 | ||||||||
|
CMplot Resource Report Resource Website 50+ mentions |
CMplot (RRID:SCR_024514) | software resource, software toolkit | Software drawing R package designed for Manhattan plot of genomic analysis. | drawing tool, Manhattan plot of genomic analysis, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/YinLiLin/CMplot | SCR_024514 | Circle Manhattan Plot | 2026-08-29 11:29:06 | 96 | ||||||||
|
maftools Resource Report Resource Website 100+ mentions |
maftools (RRID:SCR_024519) | software resource, software toolkit | Software R package offers multitude of analysis and visualization modules that are commonly used in cancer genomic studies, including driver gene identification, pathway, signature, enrichment, and association analyses. Maftools requires somatic variants in Mutation Annotation Format (MAF) and is independent of larger alignment files. | MAF summarize, MAF analyze, MAF visualize, Mutation Annotation Format files, driver gene identification, pathway, signature, enrichment, association analyses, somatic variants in Mutation Annotation Format, MAF | is listed by: SoftCite | PMID:30341162 | Free, Available for download, Freely available | https://bioconductor.org/packages/maftools/ | SCR_024519 | 2026-08-29 11:29:12 | 233 | ||||||||
|
SciPy Resource Report Resource Website 10000+ mentions |
SciPy (RRID:SCR_008058) | software application, software resource | A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console. | python, software, open source |
uses: Python Programming Language is used by: PyDSTool is used by: Elephant is used by: Stimfit is used by: Sklearn is listed by: SoftCite is related to: IPython is related to: NumPy is related to: IPython Notebook is related to: MNE software is related to: DE-Sim is required by: TomoMiner is required by: Short Read Sequence Typing for Bacterial Pathogens |
Public, Free | nif-0000-10422 | SCR_008058 | SciPy, Scientific Tools for Python | 2026-08-29 11:31:00 | 16188 | ||||||||
|
Statistical Analysis System Resource Report Resource Website 5000+ mentions |
Statistical Analysis System (RRID:SCR_008567) | SAS | data analytics software, data management software, software application, software resource | Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS. | Explore, analyze, visualize, data, standardized, management, statistics | is listed by: SoftCite | Restircted | nif-0000-31484 | https://www.sas.com/en_us/software/platform.html, https://www.sas.com/en_us/software/sas9.html | SCR_008567 | Statistical Analysis System, SAS Intelligence Platform, SAS 9.3, SAS 9.4 | 2026-08-29 11:30:50 | 7485 | ||||||
|
GENIE Resource Report Resource Website 100+ mentions |
GENIE (RRID:SCR_009197) | GENIE | software application, software resource | 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 | 2026-08-29 11:31:05 | 361 | ||||||
|
PROFILER Resource Report Resource Website 1000+ mentions |
PROFILER (RRID:SCR_009339) | PROFILER | software application, software resource | 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 | 2026-08-29 11:31:08 | 1295 | ||||||||
|
REDCap Resource Report Resource Website 10000+ mentions |
REDCap (RRID:SCR_003445) | REDCap | software resource, web application | Web application that allows users to build and manage online surveys and databases. Using REDCap's stream-lined process for rapidly developing projects, you may create and design projects using 1) the online method from your web browser using the Online Designer; and/or 2) the offline method by constructing a "data dictionary" template file in Microsoft Excel, which can be later uploaded into REDCap. Both surveys and databases (or a mixture of the two) can be built using these methods. REDCap provides audit trails for tracking data manipulation and user activity, as well as automated export procedures for seamless data downloads to Excel, PDF, and common statistical packages (SPSS, SAS, Stata, R). Also included are a built-in project calendar, a scheduling module, ad hoc reporting tools, and advanced features, such as branching logic, file uploading, and calculated fields. REDCap has a quick and easy software installation process, so that you can get REDCap running and fully functional in a matter of minutes. Several language translations have already been compiled for REDCap (e.g. Chinese, French, German, Portuguese), and it is anticipated that other languages will be available in full versions of REDCap soon. The REDCap Shared Library is a repository for REDCap data collection instruments and forms that can be downloaded and used by researchers at REDCap partner institutions. | online survey, survey, database, translational research, informatics, workflow, clinical research, clinical, metadata, biomedical, online form, data capture, management, analysis, data sharing, data collection, data standard, best practice, data collection instrument, electronic data capture |
is listed by: Biositemaps is listed by: SoftCite is related to: Clinical and Translational Science Awards Consortium has parent organization: Vanderbilt University; Tennessee; USA works with: redcap-completion works with: aux-file-upload |
NIH ; UL1 RR029882 ; UL1 TR000062 ; UL1 RR026314 ; UL1 TR000077 ; UL1 RR024975 ; UL1 TR000445 ; G12 RR003051 ; G12 MD007600 ; UL1 RR024150 ; UL1 TR000135 ; R24 HD042849 ; UL1 RR024989 ; UL1 TR000439 |
PMID:23149159 PMID:18929686 |
Software is available at no cost for REDCap Consortium Partners. If not in the consortium, See the Become a Partner page to find more information about joining our group. | nif-0000-33254 | SCR_003445 | RED Cap, Research Electronic Data Capture, The REDCap Consortium | 2026-08-29 11:28:24 | 23733 | |||||
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SRAMP Resource Report Resource Website 100+ mentions |
SRAMP (RRID:SCR_024500) | simulation software, software application, software resource | Software tool as computational predictor of mammalian m(6)A site. Used for prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features. | mammalian m(6)A site predictor, sequence derived features based predictor, | is listed by: SoftCite | PMID:26896799 | Free, Available for download, Freely available | SCR_024500 | Sequence-based Rna Adenosine Methylation site Predictor | 2026-08-29 11:28:13 | 452 | ||||||||
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RNAfold Resource Report Resource Website 100+ mentions |
RNAfold (RRID:SCR_024427) | data access protocol, software resource, web service | Web server predict secondary structures of single stranded RNA or DNA sequences. | predict secondary structures, single stranded RNA, DNA sequences, | is listed by: SoftCite | Free, Freely available | SCR_024427 | 2026-08-29 11:28:10 | 100 | ||||||||||
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Nano Measurer Resource Report Resource Website 1+ mentions |
Nano Measurer (RRID:SCR_024493) | data analysis software, data processing software, software application, software resource | Software tool to process micrograph images for particle size. | process micrograph images, images for particle size, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024493 | 2026-08-29 11:28:13 | 9 | ||||||||||
|
ToposPro Resource Report Resource Website 10+ mentions |
ToposPro (RRID:SCR_024496) | data analysis software, data processing software, software application, software resource | Software package for analysis of geometrical and topological properties of periodic structures including crystals, networks, tilings.ToposPro was tailored to process large samples of crystallographic data and to find correlations between structure parameters. | geometrical and topological properties analysis, crystals, networks, tilings, periodic structures analysis, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024496 | 2026-08-29 11:28:13 | 18 |
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