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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-orfhunter 1.20.0
Propagated dependencies: r-xfun@0.57 r-stringr@1.6.0 r-rtracklayer@1.72.0 r-rcpp@1.1.1-1.1 r-randomforest@4.7-1.2 r-peptides@2.4.6 r-data-table@1.18.4 r-bsgenome-hsapiens-ucsc-hg38@1.4.5 r-biostrings@2.80.1
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/ORFhunteR
Licenses: FSDG-compatible
Build system: r
Synopsis: Predict open reading frames in nucleotide sequences
Description:

The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. It efficiently implements the machine learning model based on vectorization of nucleotide sequences and the random forest classification algorithm. The ORFhunteR package consists of a set of functions written in the R language in conjunction with C++. The efficiency of the package was confirmed by the examples of the analysis of RNA molecules from the NCBI RefSeq and Ensembl databases. The package can be used in basic and applied biomedical research related to the study of the transcriptome of normal as well as altered (for example, cancer) human cells.

r-omiccircos 1.50.0
Propagated dependencies: r-genomicranges@1.64.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/OmicCircos
Licenses: GPL 2
Build system: r
Synopsis: High-quality circular visualization of omics data
Description:

OmicCircos is an R application and package for generating high-quality circular plots for omics data.

r-orthology-eg-db 3.23.0
Propagated dependencies: r-annotationdbi@1.74.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/Orthology.eg.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Orthology mapping package
Description:

Orthology mapping package, based on data from NCBI, using NCBI Gene IDs and Taxonomy IDs.

r-optimalflowdata 1.24.0
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-oct4 1.28.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/oct4
Licenses: GPL 2+
Build system: r
Synopsis: Conditional knockdown of OCT4 in mouse ESCs
Description:

This package provides the output of running Salmon on a set of 12 RNA-seq samples from King & Klose, "The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells", published in eLIFE, March 2017. For details on version numbers and how the samples were processed see the package vignette.

r-ontoprocdata 0.99.9901
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/ontoProcData
Licenses: Artistic License 2.0
Build system: r
Synopsis: data package for ontoProc
Description:

This package manages rda files of multiple ontologies that are used in the ontoProc package. These ontologies were originally downloaded as owl or obo files and converted into Rda files. The files were downloaded at various times but most of them were downloaded on August 08 2022.

r-opossom 2.30.0
Propagated dependencies: r-xml@3.99-0.23 r-tsne@0.2-0 r-scatterplot3d@0.3-45 r-rcurl@1.98-1.18 r-rcppparallel@5.1.11-2 r-rcpp@1.1.1-1.1 r-png@0.1-9 r-pixmap@0.4-14 r-igraph@2.3.1 r-graph@1.90.0 r-fdrtool@1.2.18 r-fastica@1.2-7 r-biomart@2.68.0 r-biobase@2.72.0 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: http://som.izbi.uni-leipzig.de
Licenses: FSDG-compatible
Build system: r
Synopsis: Comprehensive analysis of transcriptome data
Description:

This package translates microarray expression data into metadata of reduced dimension. It provides various sample-centered and group-centered visualizations, sample similarity analyses and functional enrichment analyses. The underlying SOM algorithm combines feature clustering, multidimensional scaling and dimension reduction, along with strong visualization capabilities. It enables extraction and description of functional expression modules inherent in the data.

r-org-xl-eg-db 3.23.0
Propagated dependencies: r-annotationdbi@1.74.0
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-octad 1.14.0
Propagated dependencies: r-s4vectors@0.50.1 r-ruvseq@1.46.0 r-rhdf5@2.56.0 r-rfast@2.1.5.2 r-reshape2@1.4.5 r-qpdf@1.4.1 r-plotly@4.12.0 r-octad-db@1.14.0 r-magrittr@2.0.5 r-limma@3.68.3 r-httr@1.4.8 r-htmlwidgets@1.6.4 r-gsva@2.6.2 r-ggplot2@4.0.3 r-foreach@1.5.2 r-experimenthub@3.2.0 r-edger@4.10.0 r-edaseq@2.46.0 r-dplyr@1.2.1 r-deseq2@1.52.0 r-data-table@1.18.4 r-biobase@2.72.0 r-annotationhub@4.2.0
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-opweight 1.34.0
Propagated dependencies: r-tibble@3.3.1 r-qvalue@2.44.0 r-mass@7.3-65
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://github.com/mshasan/OPWeight
Licenses: Artistic License 2.0
Build system: r
Synopsis: Optimal p-value weighting with independent information
Description:

This package perform weighted-pvalue based multiple hypothesis test and provides corresponding information such as ranking probability, weight, significant tests, etc . To conduct this testing procedure, the testing method apply a probabilistic relationship between the test rank and the corresponding test effect size.

r-ompbam 1.16.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-rcpp@1.1.1-1.1
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://github.com/alexchwong/ompBAM
Licenses: Expat
Build system: r
Synopsis: C++ Library for OpenMP-based multi-threaded sequential profiling of Binary Alignment Map (BAM) files
Description:

This packages provides C++ header files for developers wishing to create R packages that processes BAM files. ompBAM automates file access, memory management, and handling of multiple threads behind the scenes', so developers can focus on creating domain-specific functionality. The included vignette contains detailed documentation of this API, including quick-start instructions to create a new ompBAM-based package, and step-by-step explanation of the functionality behind the example packaged included within ompBAM.

r-oncomix 1.34.0
Propagated dependencies: r-summarizedexperiment@1.42.0 r-rcolorbrewer@1.1-3 r-mclust@6.1.2 r-ggrepel@0.9.8 r-ggplot2@4.0.3
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-hbacteriophora-eg-db 0.99.1
Propagated dependencies: r-dbi@1.3.0 r-annotationdbi@1.74.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://github.com/kabilanbio/org.Hbacteriophora.eg.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Genome-wide Annotation for Heterorhabditis bacteriophora
Description:

This package provides genome-wide annotation for Heterorhabditis bacteriophora, primarily based on mapping using custom gene identifiers. This OrgDb annotation package is intended for use with AnnotationDbi-based tools and supports querying of gene identifiers and related metadata.

r-oncosimulr 4.14.0
Propagated dependencies: r-stringr@1.6.0 r-smatr@3.4-8 r-rgraphviz@2.56.0 r-rcpp@1.1.1-1.1 r-rcolorbrewer@1.1-3 r-igraph@2.3.1 r-gtools@3.9.5 r-graph@1.90.0 r-ggrepel@0.9.8 r-ggplot2@4.0.3 r-dplyr@1.2.1 r-data-table@1.18.4 r-car@3.1-5
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-outsplice 1.12.0
Propagated dependencies: r-txdb-hsapiens-ucsc-hg38-knowngene@3.22.0 r-txdb-hsapiens-ucsc-hg19-knowngene@3.22.1 r-s4vectors@0.50.1 r-org-hs-eg-db@3.23.1 r-iranges@2.46.0 r-genomicranges@1.64.0 r-genomicfeatures@1.64.0 r-annotationdbi@1.74.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://github.com/GuoLabUCSD/OutSplice
Licenses: GPL 2
Build system: r
Synopsis: Comparison of Splicing Events between Tumor and Normal Samples
Description:

An easy to use tool that can compare splicing events in tumor and normal tissue samples using either a user generated matrix, or data from The Cancer Genome Atlas (TCGA). This package generates a matrix of splicing outliers that are significantly over or underexpressed in tumors samples compared to normal denoted by chromosome location. The package also will calculate the splicing burden in each tumor and characterize the types of splicing events that occur.

r-orthos 1.10.0
Propagated dependencies: r-tidyr@1.3.2 r-tensorflow@2.20.0 r-summarizedexperiment@1.42.0 r-s4vectors@0.50.1 r-rlang@1.2.0 r-reticulate@1.46.0 r-plyr@1.8.9 r-orthosdata@1.10.0 r-keras@2.16.1 r-hdf5array@1.40.0 r-ggsci@5.0.0 r-ggrepel@0.9.8 r-ggpubr@0.6.3 r-ggplot2@4.0.3 r-experimenthub@3.2.0 r-dplyr@1.2.1 r-delayedarray@0.38.1 r-cowplot@1.2.0 r-colorspace@2.1-2 r-biocparallel@1.46.0 r-basilisk@1.24.0 r-annotationhub@4.2.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/orthos
Licenses: Expat
Build system: r
Synopsis: `orthos` is an R package for variance decomposition using conditional variational auto-encoders
Description:

`orthos` decomposes RNA-seq contrasts, for example obtained from a gene knock-out or compound treatment experiment, into unspecific and experiment-specific components. Original and decomposed contrasts can be efficiently queried against a large database of contrasts (derived from ARCHS4, https://maayanlab.cloud/archs4/) to identify similar experiments. `orthos` furthermore provides plotting functions to visualize the results of such a search for similar contrasts.

r-onassisjavalibs 1.34.0
Dependencies: openjdk@25.0.2
Propagated dependencies: r-rjava@1.0-18
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/OnassisJavaLibs
Licenses: GPL 2
Build system: r
Synopsis: OnassisJavaLibs, java libraries to run conceptmapper and semantic similarity
Description:

This package provides a package that contains java libraries to call conceptmapper and compute semnatic similarity from R.

r-otubase 1.62.0
Propagated dependencies: r-vegan@2.7-3 r-shortread@1.70.0 r-s4vectors@0.50.1 r-iranges@2.46.0 r-biostrings@2.80.1 r-biobase@2.72.0
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-ocplus 1.86.0
Propagated dependencies: r-multtest@2.68.0 r-interp@1.1-6
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/OCplus
Licenses: LGPL 2.0+
Build system: r
Synopsis: Operating characteristics plus sample size and local fdr for microarray experiments
Description:

This package allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).

r-omicrexposome 1.34.0
Propagated dependencies: r-sva@3.60.0 r-summarizedexperiment@1.42.0 r-stringr@1.6.0 r-smartsva@0.1.3 r-rexposome@1.34.2 r-pma@1.2-4 r-omicade4@1.52.0 r-multidataset@1.40.0 r-limma@3.68.3 r-isva@1.10 r-gridextra@2.3 r-ggrepel@0.9.8 r-ggplot2@4.0.3 r-biobase@2.72.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/omicRexposome
Licenses: Expat
Build system: r
Synopsis: Exposome and omic data associatin and integration analysis
Description:

omicRexposome systematizes the association evaluation between exposures and omic data, taking advantage of MultiDataSet for coordinated data management, rexposome for exposome data definition and limma for association testing. Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA).

r-org-ecsakai-eg-db 3.22.0
Propagated dependencies: r-annotationdbi@1.74.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/org.EcSakai.eg.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Genome wide annotation for E coli strain Sakai
Description:

Genome wide annotation for E coli strain Sakai, primarily based on mapping using Entrez Gene identifiers.

r-obmiti 1.20.0
Propagated dependencies: r-summarizedexperiment@1.42.0 r-experimenthub@3.2.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://github.com/OmarElAshkar/ObMiTi
Licenses: GPL 3
Build system: r
Synopsis: Ob/ob Mice Data on Normal and High Fat Diet
Description:

The package provide RNA-seq count for 2 strains of mus musclus; Wild type and Ob/Ob. Each strain was divided into two groups, and each group received either chow diet or high fat diet. RNA expression was measured after 20 weeks in 7 tissues.

r-org-at-tair-db 3.22.0
Propagated dependencies: r-annotationdbi@1.74.0
Channel: guix-bioc
Location: guix-bioc/packages/o.scm (guix-bioc packages o)
Home page: https://bioconductor.org/packages/org.At.tair.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Genome wide annotation for Arabidopsis
Description:

Genome wide annotation for Arabidopsis, primarily based on mapping using TAIR identifiers.

r-pd-cyrgene-1-1-st 3.12.0
Propagated dependencies: r-s4vectors@0.50.1 r-rsqlite@3.52.0 r-oligoclasses@1.74.0 r-oligo@1.76.0 r-iranges@2.46.0 r-dbi@1.3.0 r-biostrings@2.80.1
Channel: guix-bioc
Location: guix-bioc/packages/p.scm (guix-bioc packages p)
Home page: https://bioconductor.org/packages/pd.cyrgene.1.1.st
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix CyRGene-1_1-st
Description:

Platform Design Info for Affymetrix CyRGene-1_1-st.

Page: 17677787980126
Total packages: 3017