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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Epiviz Resource Report Resource Website 1+ mentions |
Epiviz (RRID:SCR_022796) | software toolkit, software resource | Software package as interactive visualization tool for functional genomics data. Interactive visual analytics for functional genomics data. | Interactive visual analytics, functional genomics data, interactive visualization tool | is provided by: BICCN | NHGRI R01 HG006102; NHGRI R01 HG005220; Illumina Corporation ; Genentech |
PMID:25086505 | Free, Available for download, Freely available | https://bioconductor.org/packages/epivizr/, https://epiviz.github.io/ | SCR_022796 | 2026-08-09 09:08:27 | 1 | |||||||
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ggeffects Resource Report Resource Website 1+ mentions |
ggeffects (RRID:SCR_022496) | software toolkit, software resource | Software R package to create tidy data frames of marginal effects for ggplot from model outputs. Used to compute marginal effects and adjusted predictions from statistical models and returns result as tidy data frames. | Create tidy data frames of marginal effects, compute marginal effects, adjusted predictions, statistical models, tidy data frame |
is used by: ggplot2 is related to: CRAN |
Free, Available for download, Freely available | SCR_022496 | 2026-08-09 09:08:17 | 5 | ||||||||||
|
Betareg Resource Report Resource Website 1+ mentions |
Betareg (RRID:SCR_022494) | software toolkit, software resource | Software R package for modeling beta distributed dependent variables, e.g., rates and proportions. In addition to maximum likelihood regression (for both mean and precision of beta distributed response), bias corrected and bias reduced estimation as well as finite mixture models and recursive partitioning for beta regressions are provided. | Beta regression, modeling beta distributed dependent variables, rates and proportions |
is related to: CRAN is related to: R Project for Statistical Computing |
DOI:10.18637/jss.v034.i02 | Free, Available for download, Freely available | SCR_022494 | 2026-08-09 09:08:23 | 2 | |||||||||
|
monaLisa Resource Report Resource Website 1+ mentions |
monaLisa (RRID:SCR_022802) | software toolkit, software resource | Software R package to work with sequence motifs in analysis of genomics data. These include methods to annotate genomic regions or sequences with predicted motif hits and to identify motifs that drive observed changes in accessibility or expression. Functions to produce informative visualizations of obtained results are also provided. | sequence motifs, analysis of genomics data, annotate genomic regions or sequences, predicted motif hits, identify motifs | is related to: R Project for Statistical Computing | Novartis Research Foundation ; Swiss National Science Foundation ; European Research Council |
PMID:35199152 | Free, Available for download, Freely available | https://github.com/fmicompbio/monaLisa | SCR_022802 | 2026-08-09 09:08:27 | 2 | |||||||
|
TMExplorer Resource Report Resource Website |
TMExplorer (RRID:SCR_022768) | software toolkit, software resource | Software package to improve studying tumour microenvironment with single cell sequencing. Developers may use this package to obtain data for validation of new algorithms and researchers interested in tumour microenvironment may use it to study specific cancers more closely. Curated collection of scRNAseq datasets sequenced from tumours. | Curated collection of scRNAseq datasets, scRNAseq datasets sequenced from tumours, improve studying tumour microenvironment, single cell sequencing, | Free, Available for download, Freely available | SCR_022768 | Tumour Microenvironment Explorer | 2026-08-09 09:08:23 | 0 | ||||||||||
|
TALOS-N Resource Report Resource Website 1+ mentions |
TALOS-N (RRID:SCR_022800) | software toolkit, software resource | Software package for prediction of protein backbone and sidechain torsion angles from NMR chemical shifts. | Prediction of protein backbone, sidechain torsion angles, NMR chemical shifts | NIDDK | PMID:23728592 | Free, Available for download, Freely available | SCR_022800 | 2026-08-09 09:08:24 | 3 | |||||||||
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Classification And Regression Training Resource Report Resource Website 50+ mentions |
Classification And Regression Training (RRID:SCR_022524) | caret | software toolkit, software resource | Software R package that contains functions for training and plotting classification and regression models. Includes methods for pre-processing training data, calculating variable importance, and model visualizations. | training and plotting classification and regression models, pre-processing training data, calculating variable importance, model visualizations. |
is related to: CRAN is related to: R Project for Statistical Computing |
DOI:10.18637/jss.v028.i05 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/caret/ | SCR_022524 | Classification And REgression Training | 2026-08-09 09:08:24 | 54 | ||||||
|
Radiant Resource Report Resource Website 1+ mentions |
Radiant (RRID:SCR_022645) | software toolkit, software resource | Software tool used to control Plexon pattern generator for optogenetic stimulation. | control Plexon pattern generator, optogenetic stimulation, Plexon Inc. | Free, Available for download, Freely available | SCR_022645 | Radiant v2.3, Radiant v2.2 | 2026-08-09 09:08:21 | 3 | ||||||||||
|
simplePHENOTYPES Resource Report Resource Website 1+ mentions |
simplePHENOTYPES (RRID:SCR_022523) | software toolkit, software resource | Software R package that simulates pleiotropy, partial pleiotropy, and spurious pleiotropy in wide range of genetic architectures, including additive, dominance and epistatic models. Used to simulate multiple traits controlled by loci with varying degrees of pleiotropy. | Multiple traits simulation, pleiotropy, partial pleiotropy, spurious pleiotropy, causal mutations affecting multiple traits |
is related to: CRAN is related to: R Project for Statistical Computing |
NSF 1733606 | PMID:33129253 | Free, Available for download, Freely available | https://github.com/samuelbfernandes/simplePHENOTYPES | SCR_022523 | Simulation of Pleiotropic, Linked and Epistatic Phenotypes | 2026-08-09 09:08:18 | 2 | ||||||
|
ranger Resource Report Resource Website 10+ mentions |
ranger (RRID:SCR_022521) | software toolkit, software resource | Software R package as fast implementation of Random Forests for high dimentional data. | Random Forest, high dimentional data |
is related to: CRAN is related to: R Project for Statistical Computing |
DOI:10.18637/jss.v077.i01 DOI:10.48550/arXiv.1508.04409 |
Free, Available for download, Freely available | https://github.com/imbs-hl/ranger | SCR_022521 | 2026-08-09 09:08:24 | 13 | ||||||||
|
BBKNN Resource Report Resource Website 10+ mentions |
BBKNN (RRID:SCR_022807) | software application, software resource | Software to identify each cell’s top neighbours in each batch separately instead of entire cell pool with no accounting for batch. Nearest neighbours for each batch are then merged to create final list of neighbours for cell. Aligns batches in a quick and lightweight manner. | Aligns batches, nearest neighbours for each batch, identify each cell’s top neighbours, each batch separately, | is used by: scanpy | Free, Available for download, Freely available | https://github.com/Teichlab/bbknn/blob/master/docs/index.rst, https://github.com/Teichlab/bbknn | SCR_022807 | Batch Balanced KNN | 2026-08-09 09:08:05 | 20 | ||||||||
|
sctransform Resource Report Resource Website 50+ mentions |
sctransform (RRID:SCR_022146) | software toolkit, software resource | Software R package for normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. | normalization and variance stabilization, single-cell RNA-seq data, regularized negative binomial regression | DOI:10.1186/s13059-019-1874-1 | Free, Available for download, Freely available | SCR_022146 | 2026-08-09 09:08:20 | 72 | ||||||||||
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EMERALD METAGENOMICS ANNOTATIONS PIPELINE Resource Report Resource Website 1+ mentions |
EMERALD METAGENOMICS ANNOTATIONS PIPELINE (RRID:SCR_022541) | software toolkit, software resource | Software metagenomics annotations pipeline that regularly enrich up-to-date ENA and MGnify metagenomics studies with metadata extracted from research articles in EuropePMC. | Metagenomics, metagenomics annotations pipeline, ENA and MGnify metagenomics studies, metadata extracted, research articles in EuropePMC | Biotechnology and Biological Sciences Research Council | Free, Available for download, Freely available | biotools:emerald_metagenomics_annotations_pipeline | https://bio.tools/emerald_metagenomics_annotations_pipeline | SCR_022541 | 2026-08-09 09:07:58 | 1 | ||||||||
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PLR-GEN Resource Report Resource Website 1+ mentions |
PLR-GEN (RRID:SCR_022264) | software toolkit, software resource | Software package for generation of pseudo long reads by using short reads of metagenomic sample and microbial reference genome sequences as input. | pseudo long reads generation, metagenomic sample short reads, microbial reference genome sequences | Free, Available for download, Freely available | SCR_022264 | 2026-08-09 09:08:12 | 1 | |||||||||||
|
stringr Resource Report Resource Website 10+ mentions |
stringr (RRID:SCR_022813) | software toolkit, software resource | Software package to provide set of functions designed to make working with strings easy. Consistent wrappers for common string operations. | Consistent wrappers, common string operations | is listed by: CRAN | Free, Available for download, Freely available | https://CRAN.R-project.org/package=stringr | SCR_022813 | 2026-08-09 09:08:27 | 40 | |||||||||
|
FreeCAD Resource Report Resource Website 100+ mentions |
FreeCAD (RRID:SCR_022535) | software application, software resource | Open source parametric 3D modeler to design real life objects of any size. Parametric modeling allows modify your design by going back into your model history and changing its parameters. | parametric 3D modeler, design real life objects, changing model parameters | Free, Available for download, Freely available | https://github.com/FreeCAD/FreeCAD | SCR_022535 | 2026-08-09 09:07:58 | 126 | ||||||||||
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d-StructMAn Resource Report Resource Website 1+ mentions |
d-StructMAn (RRID:SCR_022534) | d-StructMAn | software application, software resource | Software tool provides annotation of non-synonymous single nucleotide variants in context of structural properties of resulting amino acid changes in corresponding proteins. Improved implementation of StructMAn, shipped in container form and extended to annotation of short in-frame indels and alterations arising as consequence of alternative splicing events. Produces range of structural features by combining information from experimentally resolved structures of many related proteins, which is unique feature of StructMAn family tools. Can also harness all protein structure models stored in AlphaFold Protein Structure Database. | Structural mutation annotation, non-synonymous single nucleotide variants annotation, non-synonymous single nucleotide variants, structural properties, amino acid changes, protein structure | Free, Available for download, Freely available | SCR_022534 | d-Structural Mutation Annotation | 2026-08-09 09:08:24 | 1 | |||||||||
|
Hi5App Resource Report Resource Website |
Hi5App (RRID:SCR_022819) | software application, software resource | Software cross platform mobile application that supports 2D/3D/4D image visualization, multi-morphometry annotation, proofreading, interactive imaging system controlling, and distributed collaboration. | 2D/3D/4D image visualization, multi-morphometry annotation, proofreading, interactive imaging system controlling, distributed collaboration | is used by: BICCN | Free, Available for download, Freely available | SCR_022819 | 2026-08-09 09:08:27 | 0 | ||||||||||
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What the Phage Resource Report Resource Website |
What the Phage (RRID:SCR_022871) | WtP | software toolkit, software resource | Parallel multitool approach for phage prediction combined with annotation and classification downstream strategy. Used for identification and analysis of phage sequences. Phage identification via nextflow and docker or singularity. | phage prediction, phage sequences analysis, phage sequences prediction | DOI:10.1101/2020.07.24.219899 | Free, Available for download, Freely available | SCR_022871 | 2026-08-09 09:08:25 | 0 | |||||||||
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SurvBenchmark Resource Report Resource Website 1+ mentions |
SurvBenchmark (RRID:SCR_022503) | software toolkit, software resource | Software package for comprehensive benchmarking study of survival analysis methods using both omics data and clinical data. Evaluates diverse collection of survival models for both clinical and omics datasets. | benchmarking study, survival analysis methods, using omics data and clinical data, survival models collection evaluation | Free, Available for download, Freely available | SCR_022503 | 2026-08-09 09:07:57 | 1 |
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