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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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R/SNP.PLOTTER Resource Report Resource Website 1+ mentions |
R/SNP.PLOTTER (RRID:SCR_009376) | software application, software resource | An R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values. Images are created as either Portable Document Format (PDF) or Encapsulated (EPS) files. (entry from Genetic Analysis Software) | gene, genetic, genomic, r | is listed by: Genetic Analysis Software | nlx_154599, SCR_009405, nlx_154649 | https://github.com/cannin/snp_plotter | http://cbdb.nimh.nih.gov/~kristin/snp.plotter.html | SCR_009376 | SNP.PLOTTER | 2026-09-05 06:32:51 | 2 | |||||||
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R/METASIM Resource Report Resource Website 1+ mentions |
R/METASIM (RRID:SCR_009370) | software application, software resource | An R package that uses an individual-based approach to simulate distributions of genotypes that result from arbitrary within and among population demographies (including extinction/recolonization). These distributions can be used to test new or existing population-genetics summary statistics or develop null distributions under various demographies. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, c++, unix, ms-windows, macos | is listed by: Genetic Analysis Software | nlx_154592 | http://linum.cofc.edu/software.html | SCR_009370 | METApopulation SIMulation | 2026-09-05 06:32:51 | 1 | ||||||||
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ROMPREV Resource Report Resource Website |
ROMPREV (RRID:SCR_009361) | ROMPREV | software application, software resource | Software tool for testing for association between polymorphisms and quantitative traits, as well as estimating trait heritability and locus-specific heritability using family data. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, any with r installation, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154577, biotools:romprev | https://bio.tools/romprev | SCR_009361 | Regression of Offspring on Mid-Parent (REVised) | 2026-09-05 06:32:51 | 0 | |||||||
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WEIGHTED FDR Resource Report Resource Website |
WEIGHTED FDR (RRID:SCR_013442) | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux, unix, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian |
nlx_154604, SCR_000848, nlx_154690, biotools:weighted_fdr | https://bio.tools/weighted_fdr | SCR_013442 | R/WEIGHTED_FDR | 2026-09-05 06:32:56 | 0 | ||||||||
|
Qvalue Resource Report Resource Website 10+ mentions |
Qvalue (RRID:SCR_001073) | data analysis software, data processing software, software application, software resource | R package that takes a list of p-values resulting from the simultaneous testing of hypotheses and estimates their q-values. It is designed to measure the proportion of false positives when a test is significant. The software is capable of generating plots for visualization. It can be applied to problems in genomics, brain imaging, astrophysics, and data mining. | p value, false positive, null hypothesis, genomics, brain imaging, astrophysics, data mining, r, visualization |
is listed by: OMICtools is hosted by: Bioconductor |
Free, Available for download, Freely available | OMICS_00624 | https://github.com/jdstorey/qvalue | SCR_001073 | 2026-09-05 06:29:53 | 32 | ||||||||
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CandiSNPer Resource Report Resource Website |
CandiSNPer (RRID:SCR_005173) | CandiSNPer | service resource, software resource, source code | A webtool which helps in characterizing Single Nucleotide Polymorphisms (SNPs) that are located in the vicinity of an SNP of interest (start SNP). Along with the computation of the maximal Linkage Disequilibrium (LD) region around the start SNP. CandiSNPer provides additional information with respect to the molecular consequences of the SNPs and the genes located in the LD region. | single nucleotide polymorphism, gene, plot, linkage disequilibrium, variant, genome-wide association study, genotyping, perl, r |
is listed by: OMICtools is related to: Ensembl has parent organization: Humboldt University of Berlin; Berlin; Germany |
PMID:20172942 | Free for academic use | OMICS_00169 | SCR_005173 | 2026-09-05 06:31:28 | 0 | |||||||
|
tsne Resource Report Resource Website 1+ mentions |
tsne (RRID:SCR_024305) | software resource, software toolkit | Softare R package as implementation of the t-SNE algorithm. | t-SNE algorithm implementation, R | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/r-cran-tsne/ | SCR_024305 | 2026-09-05 06:31:07 | 6 | |||||||||
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ENTROPY BLOCKER Resource Report Resource Website |
ENTROPY BLOCKER (RRID:SCR_000123) | ENTROPY BLOCKER | software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software application aiming at identifying haplotype blocks. The likelihood of the data is calculated minus the model complexity. The resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low. (entry from Genetic Analysis Software) | gene, genetic, genomic, r, ms-windows, linux | is listed by: Genetic Analysis Software | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_154300, nlx_154581, SCR_007247 | SCR_000123 | R/ENTROPY BLOCKER, R/ENTROPY_BLOCKER | 2026-09-05 06:31:09 | 0 | |||||||
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PLINK/SEQ Resource Report Resource Website 50+ mentions |
PLINK/SEQ (RRID:SCR_013193) | software application, software library, software resource, software toolkit | An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software) | gene, genetic, genomic, c/c++, r, macos, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: PLINK has parent organization: Harvard University; Cambridge; United States |
Open unspecified license | nlx_154213, biotools:plink-seq | https://bio.tools/plink-seq | SCR_013193 | 2026-09-05 06:30:04 | 77 | ||||||||
|
tximport Resource Report Resource Website 100+ mentions |
tximport (RRID:SCR_016752) | data analysis software, data processing software, software application, software resource | Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis. | pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools works with: edgeR works with: DESeq2 |
European Commission ; NCI T32 CA009337; SNSF 143883 |
DOI:10.12688/f1000research.7563.1 | Free, Available for download, Freely available | biotools:tximport | https://bioconductor.org/packages/tximport/, https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html, https://github.com/F1000Research/tximport, https://bio.tools/tximport | https://zenodo.org/record/35123#.W_w3behKiM8 | SCR_016752 | tximport v1.4.0 | 2026-09-05 06:30:08 | 100 | ||||
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scanpy Resource Report Resource Website 100+ mentions |
scanpy (RRID:SCR_018139) | data analysis software, data processing software, software application, software resource | Software Python tool for large scale single cell gene expression data analysis. Integrates analysis possibilities of established R-based frameworks, provides pre processing, visualization, graph-drawing and diffusion maps, clustering, identification of marker genes for clusters via differential expression tests and pseudo temporal ordering via diffusion pseudo time. | Large scale, single cell, gene expression, data analysis, R, pre processing, visualization, graph drawing, diffusion map, clustering, marker gene, differential expression test, bio.tools |
uses: BBKNN is used by: triku is used by: MUON is listed by: Debian is listed by: bio.tools is related to: Anndata has plug in: infercnvpy |
German Research Foundation ; Helmholtz Postdoc Programme |
PMID:29409532 | Free, Available for download, Freely available | biotools:scanpy, BioTools:scanpy | https://icb-scanpy.readthedocs-hosted.com/en/stable/, https://bio.tools/scanpy, https://bio.tools/scanpy, https://bio.tools/scanpy | SCR_018139 | Single Cell Analysis in Python | 2026-09-05 06:30:09 | 256 | |||||
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Rphenograph Resource Report Resource Website 10+ mentions |
Rphenograph (RRID:SCR_022603) | data analysis software, data processing software, software application, software resource | Software R tool as simple R implementation of PhenoGraph algorithm, which is clustering method designed for high dimensional single cell data analysis. | R, high dimensional single cell data analysis, clustering method |
is related to: Phenograph is related to: CRAN is related to: R Project for Statistical Computing |
Free, Available for download, Freely available | SCR_022603 | 2026-09-05 06:30:15 | 29 | ||||||||||
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RMassBank Resource Report Resource Website 1+ mentions |
RMassBank (RRID:SCR_002797) | data processing software, software application, software resource, workflow software | Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records. | standalone software, mac os x, unix/linux, windows, r, mass spectrometry, metabolomics |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Freely available, Available for download | OMICS_02657 | SCR_002797 | 2026-09-05 06:30:20 | 9 | |||||||||
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Apache Zeppelin Resource Report Resource Website 1+ mentions |
Apache Zeppelin (RRID:SCR_023637) | software resource, web application | Web based notebook that enables data driven, interactive data analytics and collaborative documents with SQL, Scala, Python, R and more. Multi purposed web based notebook which brings data ingestion, data exploration, visualization, sharing and collaboration. | notebook, data ingestion, data exploration, data visualization, interactive data analytics, collaborative documents, SQL, Scala, Python, R | Free, Available for download, Freely available | https://github.com/apache/zeppelin | SCR_023637 | 2026-09-05 06:30:25 | 1 | ||||||||||
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igraph for R Resource Report Resource Website 50+ mentions |
igraph for R (RRID:SCR_021238) | data processing software, data visualization software, network graph visualization software, software application, software resource, software toolkit | Software R package of igraph network analysis library. | Graphs analysis, network analysis, generating graph function, graph visualization, R | is related to: igraph | Free, Available for download, Freely available | SCR_021238 | rigraph, R/igraph | 2026-09-05 06:29:37 | 68 | |||||||||
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BLINK Resource Report Resource Website 1+ mentions |
BLINK (RRID:SCR_016288) | algorithm resource, data analysis software, data processing software, software application, software resource | Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power. | GWAS, SNP, dataset, r, genome, bayesian, linkage, nested, keyway, statistic, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Tutorial available | biotools:BLINK | https://bio.tools/BLINK | SCR_016288 | BLINK (Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway) | 2026-09-05 06:28:06 | 2 | |||||||
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rpy2 Resource Report Resource Website 10+ mentions |
rpy2 (RRID:SCR_024701) | software resource, source code | Software interface to use R from Python. | interface, R, Python | https://github.com/rpy2/rpy2 | SCR_024701 | 2026-09-05 06:34:39 | 11 | |||||||||||
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glmulti Resource Report Resource Website |
glmulti (RRID:SCR_025423) | software resource, software toolkit, source code | Software R package for model selection and multimodel inference. Used for automated model selection and model-averaging. Provides wrapper for glm and other functions, automatically generating all possible models with specified response and explanatory variables. | R, model selection, multimodel inference. | Free, Available for download, Freely available | SCR_025423 | 2026-09-05 06:34:58 | 0 | |||||||||||
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lme4 Resource Report Resource Website 100+ mentions |
lme4 (RRID:SCR_015654) | software resource, source code | Software R package. Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue." | linear mixed-effects model, s4 class, eigen c++ library, r package, r, bio.tools |
is listed by: CRAN is listed by: bio.tools is listed by: Debian works with: R package: lmerTest |
Free, Available for download | biotools:lme4 | https://cran.r-project.org/package=lme4, https://github.com/lme4/lme4/, https://bio.tools/lme4 | SCR_015654 | lme4, lme4.0, lme4: Linear Mixed-Effects Models using 'Eigen' and S4, lme4: Linear Mixed-Effects Models, R package: lme4 | 2026-09-05 06:34:08 | 411 | |||||||
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SomaticSignatures Resource Report Resource Website 1+ mentions |
SomaticSignatures (RRID:SCR_025620) | software resource, software toolkit, source code | Software R package for identifying mutational signatures of single nucleotide variants (SNVs) from high-throughput experiments. | R, identifying mutational signatures, single nucleotide variants, high-throughput experiments, | NSF | PMID:26163694 | Free, Available for download, Freely available, | https://github.com/juliangehring/SomaticSignatures | SCR_025620 | 2026-09-05 06:35:03 | 7 |
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