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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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miRanda Resource Report Resource Website 100+ mentions |
miRanda (RRID:SCR_017496) | data or information resource, service resource, database | Comprehensive resource of microRNA target predictions and expression profiles. Used for whole genome prediction of miRNA target genes. For each miRNA, target genes are selected on basis of sequence complementarity using position weighted local alignment algorithm, free energies of RNA-RNA duplexes, and conservation of target sites in related genomes. Provides information about set of genes potentially regulated by particular microRNA, co-occurrence of predicted target sites for multiple microRNAs in mRNA and microRNA expression profiles in tissues. Users are allowed to customize algorithm, numerical parameters, and position-specific rules., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | Whole, genome, prediction, miRNA, target, gene, expression, profile, data, FASEB list | is listed by: SoftCite | NIGMS ; Atlantic Philanthropies ; Alfred W. Bressler Scholars Endowment Fund |
PMID:18158296 | THIS RESOURCE IS NO LONGER IN SERVICE | http://www.microrna.org/microrna/home.do | SCR_017496 | MicroRNA.org. microrna.org | 2026-07-28 09:44:30 | 210 | ||||||
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riskRegression Resource Report Resource Website 10+ mentions |
riskRegression (RRID:SCR_024424) | software toolkit, software resource | Software R package provides risk regression models and prediction scores for survival analysis with competing risks. | risk prediction, risk regression models, prediction scores, survival analysis, competing risks, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/tagteam/riskRegression | SCR_024424 | 2026-07-28 09:46:06 | 11 | |||||||||
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RapGreen Resource Report Resource Website 1+ mentions |
RapGreen (RRID:SCR_024426) | PMID:34568824 | software toolkit, software resource | Software phylogenetic tree analysis package. Phylogenetic tree management, exploration and display package. | Phylogenetic tree management, phylogenetic tree analysis, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/SouthGreenPlatform/rap-green/wiki, http://southgreenplatform.github.io/rap-green/ | SCR_024426 | 2026-07-28 09:46:06 | 1 | ||||||||
|
ROCit Resource Report Resource Website 1+ mentions |
ROCit (RRID:SCR_024420) | software toolkit, software resource | Software R package for assessing overall diagnostic ability of binary classifier. Used to evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot. | assessing overall diagnostic ability of binary classifier, evaluate threshold bound metrics, construct confidence interval of ROC curve and AUC, construct empirical gains table, visualize ROC curve, visualize KS plot, visualize lift plot, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024420 | Receiver Operating Characteristic it | 2026-07-28 09:46:05 | 1 | |||||||||
|
Rgdal Resource Report Resource Website 1+ mentions |
Rgdal (RRID:SCR_024422) | software toolkit, software resource | Software R package provides bindings for the Geospatial Data Abstraction Library. Translator library for raster and vector geospatial data formats. | Translator library, geospatial data formats, Geospatial Data Abstraction Library bindings, | is listed by: SoftCite | Free, Available for download, Freely available | https://r-forge.r-project.org/projects/rgdal/ | SCR_024422 | , R geospatial data abstraction library, rgdal | 2026-07-28 09:46:09 | 3 | ||||||||
|
survivalROC Resource Report Resource Website 1+ mentions |
survivalROC (RRID:SCR_024415) | software toolkit, software resource | Software R package to compute time dependent Receiver Operating Characteristic curve from censored survival data. | compute time dependent Receiver Operating Characteristic curve, censored survival data, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024415 | survival Receiver Operating Characteristic | 2026-07-28 09:46:06 | 9 | |||||||||
|
ggridges Resource Report Resource Website 1+ mentions |
ggridges (RRID:SCR_024511) | software toolkit, software resource | Software R package enables creation of Ridgeline plots in 'ggplot2' | creation of Ridgeline plots in 'ggplot2', | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/wilkelab/ggridges | SCR_024511 | 2026-07-28 09:46:07 | 5 | |||||||||
|
gamm4 Resource Report Resource Website 1+ mentions |
gamm4 (RRID:SCR_024507) | software toolkit, software resource | Software R package to estimate generalized additive mixed models. | estimate generalized additive mixed models, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024507 | 2026-07-28 09:46:06 | 3 | ||||||||||
|
Inference of CRISPR Edits Resource Report Resource Website 50+ mentions |
Inference of CRISPR Edits (RRID:SCR_024508) | ICE | service resource, analysis service resource, production service resource, software resource | Software tool that offers analysis of CRISPR editing data. Used for inference of CRISPR edits from Sanger trace data. | analysis of CRISPR editing data, CRISPR editing analysis, | is listed by: SoftCite | PMID:35119294 | Free, Freely available | https://github.com/synthego-open/ice#ref2 | SCR_024508 | Synthego Inference of CRISPR Edits | 2026-07-28 09:46:07 | 64 | ||||||
|
Optimization Toolbox Resource Report Resource Website 1+ mentions |
Optimization Toolbox (RRID:SCR_024486) | software toolkit, software resource | Software package provides functions for finding parameters that minimize or maximize objectives while satisfying constraints. Toolbox includes solvers for linear programming, mixed integer linear programming, quadratic programming, second order cone programming, nonlinear programming, constrained linear least squares, nonlinear least squares, nonlinear equations. | Mathworks, finding parameters, minimize or maximize objectives, linear programming solver, mixed integer linear programming solver, quadratic programming solver, second order cone programming solver, nonlinear programming solver, constrained linear least squares solver, nonlinear least squares solver, nonlinear equations solver, | is listed by: SoftCite | Restricted | SCR_024486 | 2026-07-28 09:46:06 | 1 | ||||||||||
|
CopyKAT Resource Report Resource Website 50+ mentions |
CopyKAT (RRID:SCR_024512) | software toolkit, software resource | Software R package to estimate genomic copy number profiles at average genomic resolution of 5 Mb from read depth in high throughput single cell RNA sequencing data.Used for inference of genomic copy number and subclonal structure of human tumors from high-throughput single cell RNAseq data. | Inference of genomic copy number and subclonal structure of human tumors, high throughput single cell RNAseq data, | is listed by: SoftCite | PMID:33462507 | Free, Available for download, Freely available | SCR_024512 | , Copynumber Karyotyping of Aneuploid Tumors | 2026-07-28 09:46:06 | 65 | ||||||||
|
classInt Resource Report Resource Website 1+ mentions |
classInt (RRID:SCR_024515) | software toolkit, software resource | Software R package for choosing univariate class intervals for mapping or other graphics purposes. | choosing univariate class intervals, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/r-spatial/classInt/ | SCR_024515 | Class Intervals | 2026-07-28 09:46:06 | 2 | ||||||||
|
mitml Resource Report Resource Website 1+ mentions |
mitml (RRID:SCR_024516) | software toolkit, software resource | Software R package for multiple imputation of missing data in multilevel modeling. | multiple imputation of missing data in multilevel modeling, | is listed by: SoftCite | Free, Available for download, Freely available | https://github.com/simongrund1/mitml | SCR_024516 | 2026-07-28 09:46:07 | 1 | |||||||||
|
PREFAB Resource Report Resource Website 1+ mentions |
PREFAB (RRID:SCR_001009) | PREFAB | data or information resource, database | Downloadable data designed for testing multiple sequence alignment methods. | database, downloadable data, sequence alignment, sequence alignment method |
is listed by: OMICtools is listed by: SoftCite is related to: MUSCLE |
PMID:15034147 | Free, Available for download, Freely available | OMICS_00984 | SCR_001009 | PREFAB - Protein Reference Alignment Benchmark, Protein Reference Alignment Benchmark | 2026-07-28 09:40:06 | 1 | ||||||
|
GBrowse Resource Report Resource Website 10+ mentions |
GBrowse (RRID:SCR_006829) | GBrowse | data or information resource, database | A database and interactive web site for manipulating and displaying annotations on genomes. Features include: detailed views of the genome; use of a variety of premade or personally made glyphs ; customizable order and appearance of tracks by administrators and end-users; search by annotation ID, name, or comment; support of third party annotation using GFF formats; DNA and GFF dumps; connectivity to different databases, including BioSQL and Chado; and a customizable plug-in architecture (e.g. run BLAST, find oligonucleotides, design primers, etc.). GBrowse is distributed as source code for Macintosh OS X, UNIX and Linux platforms, and as pre-packaged binaries for Windows machines. It can be installed using the standard Perl module build procedure, or automated using a network-based install script. In order to use the net installer, you will need to have Perl 5.8.6 or higher and the Apache web server installed. The wiki portion accepts data submissions. | genome, annotation, database, perl, virus, dna, protein, reference sequence, chromosome, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: WormBase is related to: FlyBase is related to: International HapMap Project has parent organization: Generic Model Organism Database Project has parent organization: Indiana University; Indiana; USA |
Howard Hughes Medical Institute ; NHGRI HG00739; NHGRI P41HG02223 |
PMID:19957275 PMID:18428797 PMID:12368253 PMID:21400697 PMID:20194461 PMID:19357095 DOI:10.1002/0471250953.bi0909s28 |
The community can contribute to this resource, Requires Perl 5.8.6 or higher and the Apache web server | OMICS_00910, biotools:gbrowse, nif-0000-30597 | http://gmod.org/wiki/GBrowse, https://bio.tools/gbrowse, https://sources.debian.org/src/gbrowse/ | SCR_006829 | Generic Genome Browser | 2026-07-28 09:41:43 | 43 | ||||
|
MRIcron Resource Report Resource Website 1000+ mentions |
MRIcron (RRID:SCR_002403) | MRIcron | data visualization software, software resource, software application, data processing software | 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 | 2026-07-28 09:40:25 | 2194 | |||||
|
ModFit LT Resource Report Resource Website 100+ mentions |
ModFit LT (RRID:SCR_016106) | data visualization software, software resource, software application, data processing software | Modeling software for flow cytometry histograms. Models for cell-tracking dye studies and synchronized cell lines are built right into the software. | flow, cytometry, histogram, model, graph, cell, tracking, dye, cell line | is listed by: SoftCite | Commercially available, Available for purchase, Trial available | SCR_016106 | Verity Software House ModFit LT | 2026-07-28 09:44:09 | 143 | |||||||||
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ScanProsite Resource Report Resource Website 10+ mentions |
ScanProsite (RRID:SCR_024425) | PMID:16845026 | software resource, data access protocol, web service | Web tool for detecting PROSITE signature matches in protein sequences. | detecting PROSITE signature matches, protein sequences, | is listed by: SoftCite | Swiss National Science Foundation ; Swiss Federal Government |
Free, Freely available | https://www.expasy.org/resources/scanprosite | SCR_024425 | 2026-07-28 09:46:05 | 44 | |||||||
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VSEARCH Resource Report Resource Website 1000+ mentions |
VSEARCH (RRID:SCR_024494) | software application, software resource, data analysis software, data processing software | Software versatile open source tool for metagenomics. Used for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. | processing and preparing metagenomics, genomics and population genomics, nucleotide sequence data, | is listed by: SoftCite | PMID:27781170 | Free, Available for download, Freely available | SCR_024494 | 2026-07-28 09:46:07 | 1348 | |||||||||
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TomoStudio Resource Report Resource Website 1+ mentions |
TomoStudio (RRID:SCR_024498) | software application, software resource, data analysis software, data processing software | Software tool for acquisition and analysis, visualization and analysis of RI tomograms. Used to color code the image according to the refractive index and identify various types of quantitative data. | Tomocube, Inc., Daejeon, . Republic of Korea, visualization and analysis of RI tomograms, color code the image, | is listed by: SoftCite | Restricted | SCR_024498 | 2026-07-28 09:46:10 | 3 |
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