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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Protein preparation Wizard Resource Report Resource Website 10+ mentions |
Protein preparation Wizard (RRID:SCR_016749) | simulation software, software application, software resource | Software tool for correcting common structural problems and creating reliable, all atom protein models. | correcting, structural, problem, atom, protein, model, virtual, docking, method |
is listed by: SoftCite has parent organization: Schrodinger |
Commercially available, Training available | SCR_016749 | SciCrunch Registry | protein preparation wizard, Protein Preparation Wizard | 2026-10-24 12:49:13 | 13 | |||||||||
|
OpenEpi Resource Report Resource Website 100+ mentions |
OpenEpi (RRID:SCR_021913) | data analytics software, software application, software resource, software toolkit | Web based, open source, operating system independent series of programs designed for use in public health and medicine for training or practice that provide number of epidemiologic and statistical tools for summary data. Developed in JavaScript and HTML, and can be run in modern web browsers. Program can be run from OpenEpi website or downloaded and run without web connection. | epidemiologic tool, statistical tool, epidemiologic statistics, public health |
is listed by: SoftCite has parent organization: Emory University; Georgia; USA |
Bill and Melinda Gates Foundation | PMID:19445426 | Free, Available for download, Freely available | SCR_021913 | SciCrunch Registry | 2026-10-24 12:49:16 | 160 | ||||||||
|
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 | SciCrunch Registry | RED Cap, Research Electronic Data Capture, The REDCap Consortium | 2026-10-24 12:49:27 | 23733 | |||||
|
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 | SciCrunch Registry | 2026-10-24 12:50:17 | 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 | SciCrunch Registry | R GOplot | 2026-10-24 12:50:16 | 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 | SciCrunch Registry | generalized estimating equations pack | 2026-10-24 12:50:15 | 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 | SciCrunch Registry | 2026-10-24 12:50:17 | 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 | SciCrunch Registry | 2026-10-24 12:50:15 | 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 | SciCrunch Registry | Notung 2.9 | 2026-10-24 12:50:18 | 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 | SciCrunch Registry | Circle Manhattan Plot | 2026-10-24 12:50:17 | 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 | SciCrunch Registry | 2026-10-24 12:50:18 | 233 | ||||||||
|
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 | SciCrunch Registry | Alternative Splicing Prediction Data Base, ASPicDB - A Database tool for alternative splicing analysis | 2026-10-24 12:50:22 | 8 | ||||
|
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 | SciCrunch Registry | SAM: Significance Analysis of Microarrays, Significance Analysis of Microarrays | 2026-10-24 12:52:26 | 235 | |||||||
|
SABmark Resource Report Resource Website 1+ mentions |
SABmark (RRID:SCR_011817) | SABmark | data or information resource, data set | Downloadable data set designed to assess the performance of both multiple and pairwise (protein) sequence alignment algorithms, and is extremely easy to use. Currently, the database contains 2 sets, each consisting of a number of subsets with related sequences. It''s main features are: * Covers the entire known fold space (SCOP classification), with subsets provided by the ASTRAL compendium * All structures have high quality, with 100% resolved residues * Structure alignments have been derived carefully, using both SOFI and CE, and Relaxed Transitive Alignment * At most 25 sequences in each subset to avoid overrepresentation of large folds* Automated running, archiving and scoring of programs through a few Perl scripts The Twilight Zone set is divided into sequence groups that each represent a SCOP fold. All sequences within a group share a pairwise Blast e-value of at least 1, for a theoretical database size of 100 million residues. Sequence similarity is thus very low, between 0-25% identity, and a (traceable) common evolutionary origin cannot be established between most pairs even though their structures are (distantly) similar. This set therefore represents the worst case scenario for sequence alignment, which unfortunately is also the most frequent one, as most related sequences share less than 25% identity. The Superfamilies set consists of groups that each represent a SCOP superfamily, and therefore contain sequences with a (putative) common evolutionary origin. However, they share at most 50% identity, which is still challenging for any sequence alignment algorithm. Frequently, alignments are performed to establish whether or not sequences are related. To benchmark this, a second version of both the Twilight Zone and the Superfamilies set is provided, in which to each alignment problem a number of false positives, i.e. sequences not related to the original set, are added. Database specifications: * Current version: 1.65 (concurrent with PDB, SCOP and ASTRAL) * Twilight Zone set (with false positives): 209 groups, 1740 (3280) sequences, 10667 (44056) related pairs * Superfamilies set (with false positives): 425 groups, 3280 (6526) sequences, 19092 (79095) related pairs |
is listed by: OMICtools is listed by: SoftCite has parent organization: Vrije Universiteit Brussel; Brussels; Belgium |
PMID:15333456 | OMICS_00988 | SCR_011817 | SciCrunch Registry | SABmark - Sequence and structure Alignment Benchmark, Sequence Alignment Benchmark, Sequence and structure Alignment Benchmark | 2026-10-24 12:52:34 | 8 | ||||||||
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Stata Resource Report Resource Website 10000+ mentions |
Stata (RRID:SCR_012763) | software application, software resource | Software package for statistical analysis and presentation of graphics. Statistical software for data science. | statistical analysis, presentation of graphics, data science, | is listed by: SoftCite | Restricted | nlx_156918 | SCR_012763 | SciCrunch Registry | 2026-10-24 12:52:40 | 49366 | |||||||||
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pyPCcazip Resource Report Resource Website 1+ mentions |
pyPCcazip (RRID:SCR_024423) | software resource, source code | Software PCA-based toolkit for compression and analysis of molecular simulation data. Used for compression and analysis of molecular dynamics (MD) simulation data. | data compression and analysis, molecular simulation data, | is listed by: SoftCite | DOI:10.1016/j.softx.2016.04.002 | Free, Available for download, Freely available | SCR_024423 | SciCrunch Registry | 2026-10-24 12:53:21 | 4 |
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