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Enter the query into the form above. You can look for specific version of a package by using @ symbol like this: gcc@10.

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r-optimalflowdata 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/optimalFlowData
Licenses: Artistic License 2.0
Build system: r
Synopsis: optimalFlowData
Description:

Data files used as examples and for testing of the software provided in the optimalFlow package.

r-omicspca 1.28.0
Propagated dependencies: r-tidyr@1.3.1 r-seqinfo@1.0.0 r-rtracklayer@1.70.0 r-rmarkdown@2.30 r-rgl@1.3.31 r-reshape2@1.4.5 r-performanceanalytics@2.0.8 r-pdftools@3.6.0 r-omicspcadata@1.28.0 r-nbclust@3.0.1 r-multiassayexperiment@1.36.1 r-mass@7.3-65 r-magick@2.9.0 r-kableextra@1.4.0 r-iranges@2.44.0 r-helloranges@1.36.0 r-ggplot2@4.0.1 r-fpc@2.2-13 r-factominer@2.12 r-factoextra@1.0.7 r-data-table@1.17.8 r-cowplot@1.2.0 r-corrplot@0.95 r-clvalid@0.7 r-cluster@2.1.8.1
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/OMICsPCA
Licenses: GPL 3
Build system: r
Synopsis: An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
Description:

OMICsPCA is an analysis pipeline designed to integrate multi OMICs experiments done on various subjects (e.g. Cell lines, individuals), treatments (e.g. disease/control) or time points and to analyse such integrated data from various various angles and perspectives. In it's core OMICsPCA uses Principal Component Analysis (PCA) to integrate multiomics experiments from various sources and thus has ability to over data insufficiency issues by using the ingegrated data as representatives. OMICsPCA can be used in various application including analysis of overall distribution of OMICs assays across various samples /individuals /time points; grouping assays by user-defined conditions; identification of source of variation, similarity/dissimilarity between assays, variables or individuals.

r-oncoscore 1.38.0
Propagated dependencies: r-biomart@2.66.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://github.com/danro9685/OncoScore
Licenses: FSDG-compatible
Build system: r
Synopsis: tool to identify potentially oncogenic genes
Description:

OncoScore is a tool to measure the association of genes to cancer based on citation frequencies in biomedical literature. The score is evaluated from PubMed literature by dynamically updatable web queries.

r-osat 1.58.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: http://www.biomedcentral.com/1471-2164/13/689
Licenses: Artistic License 2.0
Build system: r
Synopsis: OSAT: Optimal Sample Assignment Tool
Description:

This package provides a sizable genomics study such as microarray often involves the use of multiple batches (groups) of experiment due to practical complication. To minimize batch effects, a careful experiment design should ensure the even distribution of biological groups and confounding factors across batches. OSAT (Optimal Sample Assignment Tool) is developed to facilitate the allocation of collected samples to different batches. With minimum steps, it produces setup that optimizes the even distribution of samples in groups of biological interest into different batches, reducing the confounding or correlation between batches and the biological variables of interest. It can also optimize the even distribution of confounding factors across batches. Our tool can handle challenging instances where incomplete and unbalanced sample collections are involved as well as ideal balanced RCBD. OSAT provides a number of predefined layout for some of the most commonly used genomics platform. Related paper can be find at http://www.biomedcentral.com/1471-2164/13/689 .

r-org-xl-eg-db 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/org.Xl.eg.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Genome wide annotation for Xenopus
Description:

Genome wide annotation for Xenopus, primarily based on mapping using Entrez Gene identifiers.

r-oncoscanr 1.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-readr@2.1.6 r-magrittr@2.0.4 r-iranges@2.44.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://github.com/yannchristinat/oncoscanR
Licenses: Expat
Build system: r
Synopsis: Secondary analyses of CNV data (HRD and more)
Description:

The software uses the copy number segments from a text file and identifies all chromosome arms that are globally altered and computes various genome-wide scores. The following HRD scores (characteristic of BRCA-mutated cancers) are included: LST, HR-LOH, nLST and gLOH. the package is tailored for the ThermoFisher Oncoscan assay analyzed with their Chromosome Alteration Suite (ChAS) but can be adapted to any input.

r-occugene 1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/occugene
Licenses: GPL 2+
Build system: r
Synopsis: Functions for Multinomial Occupancy Distribution
Description:

Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries.

r-oncosimulr 4.12.0
Propagated dependencies: r-stringr@1.6.0 r-smatr@3.4-8 r-rgraphviz@2.54.0 r-rcpp@1.1.0 r-rcolorbrewer@1.1-3 r-igraph@2.2.1 r-gtools@3.9.5 r-graph@1.88.0 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-dplyr@1.1.4 r-data-table@1.17.8 r-car@3.1-3
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://github.com/rdiaz02/OncoSimul
Licenses: GPL 3+
Build system: r
Synopsis: Forward Genetic Simulation of Cancer Progression with Epistasis
Description:

This package provides functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Fitness (including just birth, just death, or both birth and death) can also be a function of the relative and absolute frequencies of other genotypes (i.e., frequency-dependent fitness). Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulating multi-species scenarios and therapeutic interventions, including adaptive therapy, is also possible. Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Trees, Conjunctive Bayesian Networks, and other cancer progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, additive, NK, Ising, and Eggbox models) and plotting them.

r-otubase 1.60.0
Propagated dependencies: r-vegan@2.7-2 r-shortread@1.68.0 r-s4vectors@0.48.0 r-iranges@2.44.0 r-biostrings@2.78.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/OTUbase
Licenses: Artistic License 2.0
Build system: r
Synopsis: Provides structure and functions for the analysis of OTU data
Description:

This package provides a platform for Operational Taxonomic Unit based analysis.

r-omicsviewer 1.14.0
Propagated dependencies: r-survminer@0.5.1 r-survival@3.8-3 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-shinywidgets@0.9.0 r-shinythemes@1.2.0 r-shinyjs@2.1.0 r-shinycssloaders@1.1.0 r-shinybusy@0.3.3 r-shiny@1.11.1 r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-rocr@1.0-11 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-psych@2.5.6 r-plotly@4.11.0 r-openxlsx@4.2.8.1 r-networkd3@0.4.1 r-matrixstats@1.5.0 r-matrix@1.7-4 r-httr@1.4.7 r-htmlwidgets@1.6.4 r-ggseqlogo@0.2 r-ggplot2@4.0.1 r-flatxml@0.1.1 r-fgsea@1.36.0 r-fastmatch@1.1-6 r-dt@0.34.0 r-drc@3.0-1 r-curl@7.0.0 r-biobase@2.70.0 r-beeswarm@0.4.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://github.com/mengchen18/omicsViewer
Licenses: GPL 2
Build system: r
Synopsis: Interactive and explorative visualization of SummarizedExperssionSet or ExpressionSet using omicsViewer
Description:

omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way. The omicsViewer has a separate back- and front-end. In the back-end, users need to prepare an ExpressionSet that contains all the necessary information for the downstream data interpretation. Some extra requirements on the headers of phenotype data or feature data are imposed so that the provided information can be clearly recognized by the front-end, at the same time, keep a minimum modification on the existing ExpressionSet object. The pure dependency on R/Bioconductor guarantees maximum flexibility in the statistical analysis in the back-end. Once the ExpressionSet is prepared, it can be visualized using the front-end, implemented by shiny and plotly. Both features and samples could be selected from (data) tables or graphs (scatter plot/heatmap). Different types of analyses, such as enrichment analysis (using Bioconductor package fgsea or fisher's exact test) and STRING network analysis, will be performed on the fly and the results are visualized simultaneously. When a subset of samples and a phenotype variable is selected, a significance test on means (t-test or ranked based test; when phenotype variable is quantitative) or test of independence (chi-square or fisher’s exact test; when phenotype data is categorical) will be performed to test the association between the phenotype of interest with the selected samples. Additionally, other analyses can be easily added as extra shiny modules. Therefore, omicsViewer will greatly facilitate data exploration, many different hypotheses can be explored in a short time without the need for knowledge of R. In addition, the resulting data could be easily shared using a shiny server. Otherwise, a standalone version of omicsViewer together with designated omics data could be easily created by integrating it with portable R, which can be shared with collaborators or submitted as supplementary data together with a manuscript.

r-org-rn-eg-db 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/org.Rn.eg.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Genome wide annotation for Rat
Description:

Genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers.

r-oncomix 1.32.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-rcolorbrewer@1.1-3 r-mclust@6.1.2 r-ggrepel@0.9.6 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/oncomix
Licenses: GPL 3
Build system: r
Synopsis: Identifying Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data
Description:

This package helps identify mRNAs that are overexpressed in subsets of tumors relative to normal tissue. Ideal inputs would be paired tumor-normal data from the same tissue from many patients (>15 pairs). This unsupervised approach relies on the observation that oncogenes are characteristically overexpressed in only a subset of tumors in the population, and may help identify oncogene candidates purely based on differences in mRNA expression between previously unknown subtypes.

r-org-gg-eg-db 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/org.Gg.eg.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Genome wide annotation for Chicken
Description:

Genome wide annotation for Chicken, primarily based on mapping using Entrez Gene identifiers.

r-octad 1.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-ruvseq@1.44.0 r-rhdf5@2.54.0 r-rfast@2.1.5.2 r-reshape2@1.4.5 r-qpdf@1.4.1 r-plotly@4.11.0 r-octad-db@1.12.0 r-magrittr@2.0.4 r-limma@3.66.0 r-httr@1.4.7 r-htmlwidgets@1.6.4 r-gsva@2.4.1 r-ggplot2@4.0.1 r-foreach@1.5.2 r-experimenthub@3.0.0 r-edger@4.8.0 r-edaseq@2.44.0 r-dplyr@1.1.4 r-deseq2@1.50.2 r-data-table@1.17.8 r-biobase@2.70.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/octad
Licenses: Artistic License 2.0
Build system: r
Synopsis: Open Cancer TherApeutic Discovery (OCTAD)
Description:

OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene expression signature of disease by tamping down over-expressed genes and stimulating weakly expressed ones. The package offers deep-learning based reference tissue selection, disease gene expression signature creation, pathway enrichment analysis, drug reversal potency scoring, cancer cell line selection, drug enrichment analysis and in silico hit validation. It currently covers ~20,000 patient tissue samples covering 50 cancer types, and expression profiles for ~12,000 distinct compounds.

r-pwmenrich-dmelanogaster-background 4.44.0
Propagated dependencies: r-pwmenrich@4.46.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/PWMEnrich.Dmelanogaster.background
Licenses: GPL 3
Build system: r
Synopsis: D. melanogaster background for PWMEnrich
Description:

PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs.

r-pd-margene-1-0-st 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.margene.1.0.st
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix MarGene-1_0-st
Description:

Platform Design Info for Affymetrix MarGene-1_0-st.

r-pd-mg-u74bv2 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.mg.u74bv2
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for The Manufacturer's Name MG_U74Bv2
Description:

Platform Design Info for The Manufacturer's Name MG_U74Bv2.

r-pathlinkr 1.6.0
Propagated dependencies: r-visnetwork@2.1.4 r-vegan@2.7-2 r-tidyr@1.3.1 r-tidygraph@1.3.1 r-tibble@3.3.0 r-stringr@1.6.0 r-sigora@3.1.1 r-purrr@1.2.0 r-igraph@2.2.1 r-ggrepel@0.9.6 r-ggraph@2.2.2 r-ggpubr@0.6.2 r-ggplot2@4.0.1 r-ggforce@0.5.0 r-fgsea@1.36.0 r-dplyr@1.1.4 r-complexheatmap@2.26.0 r-clusterprofiler@4.18.2 r-circlize@0.4.16
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://github.com/hancockinformatics/pathlinkR
Licenses: FSDG-compatible
Build system: r
Synopsis: Analyze and interpret RNA-Seq results
Description:

pathlinkR is an R package designed to facilitate analysis of RNA-Seq results. Specifically, our aim with pathlinkR was to provide a number of tools which take a list of DE genes and perform different analyses on them, aiding with the interpretation of results. Functions are included to perform pathway enrichment, with muliplte databases supported, and tools for visualizing these results. Genes can also be used to create and plot protein-protein interaction networks, all from inside of R.

r-planet 1.18.0
Propagated dependencies: r-tibble@3.3.0 r-magrittr@2.0.4 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: http://github.com/wvictor14/planet
Licenses: GPL 2
Build system: r
Synopsis: Placental DNA methylation analysis tools
Description:

This package contains R functions to predict biological variables to from placnetal DNA methylation data generated from infinium arrays. This includes inferring ethnicity/ancestry, gestational age, and cell composition from placental DNA methylation array (450k/850k) data.

r-pd-porcine 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.porcine
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for The Manufacturer's Name Porcine
Description:

Platform Design Info for The Manufacturer's Name Porcine.

r-pd-mogene-2-1-st 3.14.1
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.mogene.2.1.st
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix MoGene-2_1-st
Description:

Platform Design Info for Affymetrix MoGene-2_1-st.

r-pd-guigene-1-0-st 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.guigene.1.0.st
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix GuiGene-1_0-st
Description:

Platform Design Info for Affymetrix GuiGene-1_0-st.

r-padog 1.52.0
Propagated dependencies: r-nlme@3.1-168 r-limma@3.66.0 r-keggrest@1.50.0 r-keggdzpathwaysgeo@1.48.0 r-hgu133plus2-db@3.13.0 r-hgu133a-db@3.13.0 r-gsa@1.03.3 r-foreach@1.5.2 r-dorng@1.8.6.2 r-biobase@2.70.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/PADOG
Licenses: GPL 2+
Build system: r
Synopsis: Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
Description:

This package implements a general purpose gene set analysis method called PADOG that downplays the importance of genes that apear often accross the sets of genes to be analyzed. The package provides also a benchmark for gene set analysis methods in terms of sensitivity and ranking using 24 public datasets from KEGGdzPathwaysGEO package.

r-pd-zebgene-1-0-st 3.12.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-oligoclasses@1.72.0 r-oligo@1.74.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.zebgene.1.0.st
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix ZebGene-1_0-st
Description:

Platform Design Info for Affymetrix ZebGene-1_0-st.

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