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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-rtnsurvival 1.34.0
Propagated dependencies: r-survival@3.8-3 r-scales@1.4.0 r-rtnduals@1.34.0 r-rtn@2.34.0 r-rcolorbrewer@1.1-3 r-pheatmap@1.0.13 r-ggplot2@4.0.1 r-egg@0.4.5 r-dunn-test@1.3.6 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RTNsurvival
Licenses: Artistic License 2.0
Build system: r
Synopsis: Survival analysis using transcriptional networks inferred by the RTN package
Description:

RTNsurvival is a tool for integrating regulons generated by the RTN package with survival information. For a given regulon, the 2-tailed GSEA approach computes a differential Enrichment Score (dES) for each individual sample, and the dES distribution of all samples is then used to assess the survival statistics for the cohort. There are two main survival analysis workflows: a Cox Proportional Hazards approach used to model regulons as predictors of survival time, and a Kaplan-Meier analysis assessing the stratification of a cohort based on the regulon activity. All plots can be fine-tuned to the user's specifications.

r-readqpcr 1.56.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://www.bioconductor.org/packages/release/bioc/html/ReadqPCR.html
Licenses: LGPL 3
Build system: r
Synopsis: Read qPCR data
Description:

The package provides functions to read raw RT-qPCR data of different platforms.

r-rontotools 2.38.0
Propagated dependencies: r-rgraphviz@2.54.0 r-keggrest@1.50.0 r-kegggraph@1.70.0 r-graph@1.88.0 r-boot@1.3-32
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/ROntoTools
Licenses: FSDG-compatible
Build system: r
Synopsis: R Onto-Tools suite
Description:

Suite of tools for functional analysis.

r-rfastp 1.20.1
Propagated dependencies: r-rjson@0.2.23 r-rhtslib@3.6.0 r-reshape2@1.4.5 r-rcpp@1.1.0 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/Rfastp
Licenses: FSDG-compatible
Build system: r
Synopsis: An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing)
Description:

Rfastp is an R wrapper of fastp developed in c++. fastp performs quality control for fastq files. including low quality bases trimming, polyX trimming, adapter auto-detection and trimming, paired-end reads merging, UMI sequence/id handling. Rfastp can concatenate multiple files into one file (like shell command cat) and accept multiple files as input.

r-rforproteomics 1.48.0
Propagated dependencies: r-r-utils@2.13.0 r-msnbase@2.36.0 r-biocviews@1.78.0 r-biocmanager@1.30.27
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://lgatto.github.com/RforProteomics/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication
Description:

This package contains code to illustrate the Using R and Bioconductor for proteomics data analysis and Visualisation of proteomics data using R and Bioconductor manuscripts. The vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation. It also contain various function to discover R software for mass spectrometry and proteomics.

r-rificomparative 1.10.0
Propagated dependencies: r-writexl@1.5.4 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rlang@1.1.6 r-reshape2@1.4.5 r-nnet@7.3-20 r-lsd@4.1-0 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-foreach@1.5.2 r-egg@0.4.5 r-dta@2.56.0 r-dplyr@1.1.4 r-domc@1.3.8 r-devtools@2.4.6 r-cowplot@1.2.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rifiComparative
Licenses: FSDG-compatible
Build system: r
Synopsis: 'rifiComparative' compares the output of rifi from two different conditions
Description:

rifiComparative is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.

r-rgug4130a-db 3.2.3
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rgug4130a.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Agilent Rat annotation data (chip rgug4130a)
Description:

Agilent Rat annotation data (chip rgug4130a) assembled using data from public repositories.

r-rsweep 1.22.0
Propagated dependencies: r-stringi@1.8.7 r-foreach@1.5.2 r-doparallel@1.0.17 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rSWeeP
Licenses: GPL 2+
Build system: r
Synopsis: Spaced Words Projection (SWeeP)
Description:

"Spaced Words Projection (SWeeP)" is a method for representing biological sequences using vectors preserving inter-sequence comparability.

r-rawrr 1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/fgcz/rawrr/
Licenses: GPL 3
Build system: r
Synopsis: Direct Access to Orbitrap Data and Beyond
Description:

This package wraps the functionality of the Thermo Fisher Scientic RawFileReader .NET 8.0 assembly. Within the R environment, spectra and chromatograms are represented by S3 objects. The package provides basic functions to download and install the required third-party libraries. The package is developed, tested, and used at the Functional Genomics Center Zurich, Switzerland.

r-rexposome 1.32.0
Propagated dependencies: r-stringr@1.6.0 r-scatterplot3d@0.3-44 r-scales@1.4.0 r-s4vectors@0.48.0 r-reshape2@1.4.5 r-pryr@0.1.6 r-mice@3.18.0 r-lsr@0.5.2 r-lme4@1.1-37 r-imputelcmd@2.1 r-hmisc@5.2-4 r-gtools@3.9.5 r-gridextra@2.3 r-gplots@3.2.0 r-glmnet@4.1-10 r-ggridges@0.5.7 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-factominer@2.12 r-corrplot@0.95 r-circlize@0.4.16 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rexposome
Licenses: Expat
Build system: r
Synopsis: Exposome exploration and outcome data analysis
Description:

Package that allows to explore the exposome and to perform association analyses between exposures and health outcomes.

r-rguatlas4k-db 3.2.3
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rguatlas4k.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Clontech BD Atlas Long Oligos Rat 4K annotation data (chip rguatlas4k)
Description:

Clontech BD Atlas Long Oligos Rat 4K annotation data (chip rguatlas4k) assembled using data from public repositories.

r-rtopper 1.56.0
Propagated dependencies: r-multtest@2.66.0 r-limma@3.66.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RTopper
Licenses: FSDG-compatible
Build system: r
Synopsis: This package is designed to perform Gene Set Analysis across multiple genomic platforms
Description:

the RTopper package is designed to perform and integrate gene set enrichment results across multiple genomic platforms.

r-resolve 1.12.0
Propagated dependencies: r-survival@3.8-3 r-s4vectors@0.48.0 r-rhpcblasctl@0.23-42 r-reshape2@1.4.5 r-nnls@1.6 r-mutationalpatterns@3.19.1 r-lsa@0.73.3 r-iranges@2.44.0 r-gridextra@2.3 r-glmnet@4.1-10 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-data-table@1.17.8 r-cluster@2.1.8.1 r-bsgenome-hsapiens-1000genomes-hs37d5@0.99.1 r-bsgenome@1.78.0 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/danro9685/RESOLVE
Licenses: FSDG-compatible
Build system: r
Synopsis: RESOLVE: An R package for the efficient analysis of mutational signatures from cancer genomes
Description:

Cancer is a genetic disease caused by somatic mutations in genes controlling key biological functions such as cellular growth and division. Such mutations may arise both through cell-intrinsic and exogenous processes, generating characteristic mutational patterns over the genome named mutational signatures. The study of mutational signatures have become a standard component of modern genomics studies, since it can reveal which (environmental and endogenous) mutagenic processes are active in a tumor, and may highlight markers for therapeutic response. Mutational signatures computational analysis presents many pitfalls. First, the task of determining the number of signatures is very complex and depends on heuristics. Second, several signatures have no clear etiology, casting doubt on them being computational artifacts rather than due to mutagenic processes. Last, approaches for signatures assignment are greatly influenced by the set of signatures used for the analysis. To overcome these limitations, we developed RESOLVE (Robust EStimation Of mutationaL signatures Via rEgularization), a framework that allows the efficient extraction and assignment of mutational signatures. RESOLVE implements a novel algorithm that enables (i) the efficient extraction, (ii) exposure estimation, and (iii) confidence assessment during the computational inference of mutational signatures.

r-ritan 1.34.0
Propagated dependencies: r-stringdb@2.22.0 r-sqldf@0.4-11 r-ritandata@1.34.0 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-png@0.1-8 r-plotrix@3.8-13 r-mcl@1.0 r-knitr@1.50 r-igraph@2.2.1 r-hash@2.2.6.3 r-gsubfn@0.7 r-gridextra@2.3 r-gplots@3.2.0 r-ggplot2@4.0.1 r-genomicfeatures@1.62.0 r-ensembldb@2.34.0 r-ensdb-hsapiens-v86@2.99.0 r-dynamictreecut@1.63-1 r-bgeedb@2.36.0 r-annotationfilter@1.34.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RITAN
Licenses: FSDG-compatible
Build system: r
Synopsis: Rapid Integration of Term Annotation and Network resources
Description:

This package provides tools for comprehensive gene set enrichment and extraction of multi-resource high confidence subnetworks. RITAN facilitates bioinformatic tasks for enabling network biology research.

r-r3cpet 1.42.0
Propagated dependencies: r-s4vectors@0.48.0 r-reshape2@1.4.5 r-rcurl@1.98-1.17 r-rcpp@1.1.0 r-pheatmap@1.0.13 r-iranges@2.44.0 r-igraph@2.2.1 r-hmisc@5.2-4 r-ggplot2@4.0.1 r-ggbio@1.58.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-data-table@1.17.8 r-clvalid@0.7 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/R3CPET
Licenses: FSDG-compatible
Build system: r
Synopsis: 3CPET: Finding Co-factor Complexes in Chia-PET experiment using a Hierarchical Dirichlet Process
Description:

The package provides a method to infer the set of proteins that are more probably to work together to maintain chormatin interaction given a ChIA-PET experiment results.

r-rain 1.44.0
Propagated dependencies: r-multtest@2.66.0 r-gmp@0.7-5
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rain
Licenses: GPL 2
Build system: r
Synopsis: Rhythmicity Analysis Incorporating Non-parametric Methods
Description:

This package uses non-parametric methods to detect rhythms in time series. It deals with outliers, missing values and is optimized for time series comprising 10-100 measurements. As it does not assume expect any distinct waveform it is optimal or detecting oscillating behavior (e.g. circadian or cell cycle) in e.g. genome- or proteome-wide biological measurements such as: micro arrays, proteome mass spectrometry, or metabolome measurements.

r-rmelting 1.26.0
Dependencies: openjdk@25
Propagated dependencies: r-rjava@1.0-11 r-rdpack@2.6.4
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/aravind-j/rmelting
Licenses: GPL 2 GPL 3
Build system: r
Synopsis: R Interface to MELTING 5
Description:

R interface to the MELTING 5 program (https://www.ebi.ac.uk/biomodels/tools/melting/) to compute melting temperatures of nucleic acid duplexes along with other thermodynamic parameters.

r-reactomegsa-data 1.24.0
Propagated dependencies: r-seurat@5.3.1 r-reactomegsa@1.24.1 r-limma@3.66.0 r-edger@4.8.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/reactome/ReactomeGSA.data/issues
Licenses: Artistic License 2.0
Build system: r
Synopsis: Companion data package for the ReactomeGSA package
Description:

Companion data sets to showcase the functionality of the ReactomeGSA package. This package contains proteomics and RNA-seq data of the melanoma B-cell induction study by Griss et al. and scRNA-seq data from Jerby-Arnon et al.

r-rat-db0 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rat.db0
Licenses: Artistic License 2.0
Build system: r
Synopsis: Base Level Annotation databases for rat
Description:

Base annotation databases for rat, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

r-ribodipa 1.18.0
Propagated dependencies: r-txdbmaker@1.6.0 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-reldist@1.7-2 r-rcpp@1.1.0 r-qvalue@2.42.0 r-matrixstats@1.5.0 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0 r-foreach@1.5.2 r-elitism@1.1.1 r-doparallel@1.0.17 r-deseq2@1.50.2 r-data-table@1.17.8 r-biocgenerics@0.56.0 r-biocfilecache@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RiboDiPA
Licenses: LGPL 3+
Build system: r
Synopsis: Differential pattern analysis for Ribo-seq data
Description:

This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization.

r-reconsi 1.22.0
Propagated dependencies: r-reshape2@1.4.5 r-phyloseq@1.54.0 r-matrixstats@1.5.0 r-matrix@1.7-4 r-ks@1.15.1 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/reconsi
Licenses: GPL 2
Build system: r
Synopsis: Resampling Collapsed Null Distributions for Simultaneous Inference
Description:

Improves simultaneous inference under dependence of tests by estimating a collapsed null distribution through resampling. Accounting for the dependence between tests increases the power while reducing the variability of the false discovery proportion. This dependence is common in genomics applications, e.g. when combining flow cytometry measurements with microbiome sequence counts.

r-rtcga-rppa 1.38.0
Propagated dependencies: r-rtcga@1.40.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RTCGA.RPPA
Licenses: GPL 2
Build system: r
Synopsis: RPPA datasets from The Cancer Genome Atlas Project
Description:

Package provides RPPA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Protein+Array +Data+Format+Specification?src=search.

r-rols 3.6.1
Propagated dependencies: r-jsonlite@2.0.0 r-httr2@1.2.1 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://lgatto.github.io/rols/
Licenses: GPL 2
Build system: r
Synopsis: An R interface to the Ontology Lookup Service
Description:

The rols package is an interface to the Ontology Lookup Service (OLS) to access and query hundred of ontolgies directly from R.

r-ruvcorr 1.42.0
Propagated dependencies: r-snowfall@1.84-6.3 r-reshape2@1.4.5 r-psych@2.5.6 r-mass@7.3-65 r-lattice@0.22-7 r-gridextra@2.3 r-corrplot@0.95 r-bladderbatch@1.48.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RUVcorr
Licenses: GPL 2
Build system: r
Synopsis: Removal of unwanted variation for gene-gene correlations and related analysis
Description:

RUVcorr allows to apply global removal of unwanted variation (ridged version of RUV) to real and simulated gene expression data.

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