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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Agilent Seahorse Wave Resource Report Resource Website 10+ mentions |
Agilent Seahorse Wave (RRID:SCR_024491) | data acquisition software, data processing software, software application, software resource | Instrument control and data acquisition software for Agilent Seahorse XFe96 and XFe24 analyzers with Windows 10 64-bit OS only. Experiment design, instrument control, data analysis, and file management software. Software provides intuitive interface with predefined assay templates and streamlined experimental design for simplified metabolic analysis. | Instrument control, data acquisition, Agilent Seahorse XFe96 analyzer, Agilent Seahorse XFe24 analyzer, predefined assay templates, streamlined experimental design, simplified metabolic analysis, | is listed by: SoftCite | SCR_024491 | SciCrunch Registry | Seahorse Wave | 2026-11-07 12:01:16 | 27 | ||||||||||
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lDDT Resource Report Resource Website 1+ mentions |
lDDT (RRID:SCR_024524) | data access protocol, software resource, web service | Web server for local superposition free score for comparing protein structures and models using distance difference tests. Superposition free score that evaluates local distance differences of all atoms in model, including validation of stereochemical plausibility. | local superposition free score, comparing protein structures and models, distance difference tests, | is listed by: SoftCite | PMID:23986568 | Free, Freely available | SCR_024524 | SciCrunch Registry | Local Distance Difference Test | 2026-11-07 12:01:18 | 2 | ||||||||
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SimPhy Resource Report Resource Website 1+ mentions |
SimPhy (RRID:SCR_024501) | simulation software, software application, software resource | Software package for simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer, all three potentially leading to species tree/gene tree discordance and gene conversion. Used for phylogenomic simulation of gene, locus, and species trees. | phylogenomic simulation, gene phylogenomic simulation, locus phylogenomic simulation, species trees phylogenomic simulation, | is listed by: SoftCite | PMID:26526427 | Free, Available for download, Freely available | SCR_024501 | SciCrunch Registry | 2026-11-07 12:01:16 | 1 | |||||||||
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Mutation Assessor Resource Report Resource Website 500+ mentions |
Mutation Assessor (RRID:SCR_024502) | software resource, web application | Web server predicts functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. Functional impact is assessed based on evolutionary conservation of affected amino acid in protein homologs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | functional impact of amino-acid substitutions in proteins prediction, | is listed by: SoftCite | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_024502 | SciCrunch Registry | 2026-11-07 12:01:18 | 535 | ||||||||||
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CRISPResso2 Resource Report Resource Website 50+ mentions |
CRISPResso2 (RRID:SCR_024503) | data analysis software, data processing software, software application, software resource | Software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. | sequencing data analysis, genome editing experiments interpretation, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024503 | SciCrunch Registry | 2026-11-07 12:00:59 | 61 | ||||||||||
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OpenBUGS Resource Report Resource Website 100+ mentions |
OpenBUGS (RRID:SCR_024488) | data analysis software, data processing software, software application, software resource | Software for analysing complex statistical models using Markov chain Monte Carlo methods. | analysing complex statistical models, Markov chain Monte Carlo method, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024488 | SciCrunch Registry | Open Bayesian inference Using Gibbs Sampling | 2026-11-07 12:01:18 | 161 | |||||||||
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AutoRT Resource Report Resource Website 1+ mentions |
AutoRT (RRID:SCR_024513) | simulation software, software application, software resource | Software tool for peptide retention time prediction using deep learning. Supports peptide retention prediction for tryptic peptides, MHC bound peptides and PTM peptides. | proteogenomics analysis | is listed by: SoftCite | PMID:32273506 | Free, Available for download, Freely available | SCR_024513 | SciCrunch Registry | 2026-11-07 12:01:15 | 3 | |||||||||
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ModFOLD Resource Report Resource Website 1+ mentions |
ModFOLD (RRID:SCR_024518) | data access protocol, software resource, web service | Web server for the global and local quality estimation of 3D protein models | quality estimation, 3D protein models, | is listed by: SoftCite | PMID:28460136 | Restricted | SCR_024518 | SciCrunch Registry | ModFOLD6, ModFOLD8 | 2026-11-07 12:01:16 | 5 | ||||||||
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Metscape Resource Report Resource Website 100+ mentions |
Metscape (RRID:SCR_014687) | resource, software resource, source code | A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data. | metabolomics, metabolomics tool, visualization, expression profiling, gene, compound, metabolism, human |
is listed by: Metabolomics Workbench is listed by: SoftCite |
NIDDK U24 DK097153; NIDDK P30DK089503 |
PMID:22135418 | Freely available | SCR_014687 | SciCrunch Registry | 2026-11-07 12:01:20 | 154 | ||||||||
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MINC Resource Report Resource Website 100+ mentions |
MINC (RRID:SCR_002391) | MINC | data processing software, image analysis software, software application, software resource | A medical imaging data format and an associated set of tools and libraries including a 3 level API for medical image analysis with a particular focus on the needs of research. There are also a number of tools including Registration and Non-Uniformity correction. | reusable library, c, file format, fortran, information specification, minc, minc2, magnetic resonance, os independent, perl, sh/bash, unix shell |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: SoftCite is related to: MINC Example files is related to: Extensible MATLAB Medical image Analysis has parent organization: McConnell Brain Imaging Center |
Free, Available for download, Freely available | nlx_155794 | http://www.nitrc.org/projects/minc | SCR_002391 | SciCrunch Registry | MINC - Medical Image NetCDF, Medical Imaging NetCDF | 2026-11-07 12:01:23 | 126 | ||||||
|
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 | 2026-11-07 12:02:11 | 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 | 2026-11-07 12:02:10 | 415 | |||||||
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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 | 2026-11-07 12:02:00 | 3 | |||||||||
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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 | 2026-11-07 12:02:10 | 25 | ||||||||
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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 | 2026-11-07 12:02:00 | 1 | |||||||||
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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 | 2026-11-07 12:01:52 | 9 | ||||||||
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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 | 2026-11-07 12:02:10 | 96 | ||||||||
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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 | 2026-11-07 12:01:52 | 233 | ||||||||
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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 | 2026-11-07 12:01:59 | 8 | ||||
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T-Coffee Resource Report Resource Website 1000+ mentions |
T-Coffee (RRID:SCR_011818) | T-Coffee | analysis service resource, data analysis service, production service resource, service resource | A multiple sequence alignment server which can align Protein, DNA and RNA sequences. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:10964570 DOI:10.1006/jmbi.2000.4042 |
biotools:tcoffee, OMICS_00989 | https://bio.tools/tcoffee, https://sources.debian.org/src/t-coffee/ | SCR_011818 | SciCrunch Registry | T-Coffee: Aligns DNA RNA or Proteins using the default T-Coffee | 2026-11-07 12:03:13 | 1157 |
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