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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-rcwlpipelines 1.26.0
Dependencies: node@22.14.0
Propagated dependencies: r-s4vectors@0.46.0 r-rcwl@1.26.0 r-rappdirs@0.3.3 r-httr@1.4.7 r-git2r@0.36.2 r-biocfilecache@2.16.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RcwlPipelines
Licenses: GPL 2
Synopsis: Bioinformatics pipelines based on Rcwl
Description:

This package provides a collection of Bioinformatics tools and pipelines based on R and the Common Workflow Language.

r-rnadecay 1.30.0
Propagated dependencies: r-tmb@1.9.17 r-scales@1.4.0 r-nloptr@2.2.1 r-gplots@3.2.0 r-ggplot2@3.5.2
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RNAdecay
Licenses: GPL 2
Synopsis: Maximum Likelihood Decay Modeling of RNA Degradation Data
Description:

RNA degradation is monitored through measurement of RNA abundance after inhibiting RNA synthesis. This package has functions and example scripts to facilitate (1) data normalization, (2) data modeling using constant decay rate or time-dependent decay rate models, (3) the evaluation of treatment or genotype effects, and (4) plotting of the data and models. Data Normalization: functions and scripts make easy the normalization to the initial (T0) RNA abundance, as well as a method to correct for artificial inflation of Reads per Million (RPM) abundance in global assessments as the total size of the RNA pool decreases. Modeling: Normalized data is then modeled using maximum likelihood to fit parameters. For making treatment or genotype comparisons (up to four), the modeling step models all possible treatment effects on each gene by repeating the modeling with constraints on the model parameters (i.e., the decay rate of treatments A and B are modeled once with them being equal and again allowing them to both vary independently). Model Selection: The AICc value is calculated for each model, and the model with the lowest AICc is chosen. Modeling results of selected models are then compiled into a single data frame. Graphical Plotting: functions are provided to easily visualize decay data model, or half-life distributions using ggplot2 package functions.

r-rcm 1.26.0
Propagated dependencies: r-vgam@1.1-13 r-tseries@0.10-58 r-tensor@1.5 r-reshape2@1.4.4 r-rcolorbrewer@1.1-3 r-phyloseq@1.52.0 r-nleqslv@3.3.5 r-mass@7.3-65 r-ggplot2@3.5.2 r-edger@4.6.2 r-alabama@2023.1.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/release/bioc/vignettes/RCM/inst/doc/RCMvignette.html/
Licenses: GPL 2
Synopsis: Fit row-column association models with the negative binomial distribution for the microbiome
Description:

Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis. In addition, diagnostic plot to detect lack of fit are available.

r-rrdp 1.44.0
Propagated dependencies: r-rjava@1.0-11 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/mhahsler/rRDP/
Licenses: FSDG-compatible
Synopsis: Interface to the RDP Classifier
Description:

This package installs and interfaces the naive Bayesian classifier for 16S rRNA sequences developed by the Ribosomal Database Project (RDP). With this package the classifier trained with the standard training set can be used or a custom classifier can be trained.

r-rmspc 1.16.0
Propagated dependencies: r-stringr@1.5.1 r-rtracklayer@1.68.0 r-processx@3.8.6 r-genomicranges@1.60.0 r-biocmanager@1.30.25
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://genometric.github.io/MSPC/
Licenses: GPL 3
Synopsis: Multiple Sample Peak Calling
Description:

The rmspc package runs MSPC (Multiple Sample Peak Calling) software using R. The analysis of ChIP-seq samples outputs a number of enriched regions (commonly known as "peaks"), each indicating a protein-DNA interaction or a specific chromatin modification. When replicate samples are analyzed, overlapping peaks are expected. This repeated evidence can therefore be used to locally lower the minimum significance required to accept a peak. MSPC uses combined evidence from replicated experiments to evaluate peak calling output, rescuing peaks, and reduce false positives. It takes any number of replicates as input and improves sensitivity and specificity of peak calling on each, and identifies consensus regions between the input samples.

r-r3cpet 1.42.0
Propagated dependencies: r-s4vectors@0.46.0 r-reshape2@1.4.4 r-rcurl@1.98-1.17 r-rcpp@1.0.14 r-pheatmap@1.0.12 r-iranges@2.42.0 r-igraph@2.1.4 r-hmisc@5.2-3 r-ggplot2@3.5.2 r-ggbio@1.56.0 r-genomicranges@1.60.0 r-genomeinfodb@1.44.0 r-data-table@1.17.4 r-clvalid@0.7 r-biocgenerics@0.54.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/R3CPET
Licenses: FSDG-compatible
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-rgu34acdf 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rgu34acdf
Licenses: LGPL 2.0+
Synopsis: rgu34acdf
Description:

This package provides a package containing an environment representing the RG_U34A.cdf file.

r-rsvsim 1.50.0
Propagated dependencies: r-shortread@1.66.0 r-iranges@2.42.0 r-genomicranges@1.60.0 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RSVSim
Licenses: LGPL 3
Synopsis: RSVSim: an R/Bioconductor package for the simulation of structural variations
Description:

RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.

r-rat2302-db 3.13.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rat2302.db
Licenses: Artistic License 2.0
Synopsis: Affymetrix Affymetrix Rat230_2 Array annotation data (chip rat2302)
Description:

Affymetrix Affymetrix Rat230_2 Array annotation data (chip rat2302) assembled using data from public repositories.

r-rtrm 1.48.0
Propagated dependencies: r-rsqlite@2.3.11 r-igraph@2.1.4 r-dbi@1.2.3 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/ddiez/rTRM
Licenses: GPL 3
Synopsis: Identification of Transcriptional Regulatory Modules from Protein-Protein Interaction Networks
Description:

rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.

r-raids 1.8.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://krasnitzlab.github.io/RAIDS/
Licenses: FSDG-compatible
Synopsis: Robust Ancestry Inference using Data Synthesis
Description:

This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.

r-rtu34probe 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rtu34probe
Licenses: LGPL 2.0+
Synopsis: Probe sequence data for microarrays of type rtu34
Description:

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RT-U34\_probe\_tab.

r-rcx 1.14.0
Propagated dependencies: r-plyr@1.8.9 r-jsonlite@2.0.0 r-igraph@2.1.4
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/frankkramer-lab/RCX
Licenses: Expat
Synopsis: R package implementing the Cytoscape Exchange (CX) format
Description:

Create, handle, validate, visualize and convert networks in the Cytoscape exchange (CX) format to standard data types and objects. The package also provides conversion to and from objects of iGraph and graphNEL. The CX format is also used by the NDEx platform, a online commons for biological networks, and the network visualization software Cytocape.

r-ragene10stprobeset-db 8.8.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/ragene10stprobeset.db
Licenses: Artistic License 2.0
Synopsis: Affymetrix ragene10 annotation data (chip ragene10stprobeset)
Description:

Affymetrix ragene10 annotation data (chip ragene10stprobeset) assembled using data from public repositories.

r-rbiopaxparser 2.50.0
Propagated dependencies: r-xml@3.99-0.18 r-data-table@1.17.4
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/frankkramer-lab/rBiopaxParser
Licenses: GPL 2+
Synopsis: Parses BioPax files and represents them in R
Description:

Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.

r-rtcga-pancan12 1.38.0
Propagated dependencies: r-rtcga@1.38.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RTCGA.PANCAN12
Licenses: GPL 2
Synopsis: PanCan 12 from Genome Cancer Browser
Description:

Package provides clinical, expression, cnv and mutation data from Genome Cancer Browser.

r-rnbeads-mm9 1.42.0
Propagated dependencies: r-genomicranges@1.60.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RnBeads.mm9
Licenses: GPL 3
Synopsis: RnBeads.mm9
Description:

Automatically generated RnBeads annotation package for the assembly mm9.

r-rwikipathways 1.30.0
Propagated dependencies: r-xml@3.99-0.18 r-tidyr@1.3.1 r-stringr@1.5.1 r-rjson@0.2.23 r-readr@2.1.5 r-rcurl@1.98-1.17 r-purrr@1.0.4 r-lubridate@1.9.4 r-httr@1.4.7 r-dplyr@1.1.4 r-data-table@1.17.4
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/wikipathways/rWikiPathways
Licenses: Expat
Synopsis: rWikiPathways - R client library for the WikiPathways API
Description:

Use this package to interface with the WikiPathways API. It provides programmatic access to WikiPathways content in multiple data and image formats, including official monthly release files and convenient GMT read/write functions.

r-rsemmed 1.20.0
Propagated dependencies: r-stringr@1.5.1 r-magrittr@2.0.3 r-igraph@2.1.4 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/lmyint/rsemmed
Licenses: Artistic License 2.0
Synopsis: An interface to the Semantic MEDLINE database
Description:

This package provides a programmatic interface to the Semantic MEDLINE database. It provides functions for searching the database for concepts and finding paths between concepts. Path searching can also be tailored to user specifications, such as placing restrictions on concept types and the type of link between concepts. It also provides functions for summarizing and visualizing those paths.

r-rforproteomics 1.48.0
Propagated dependencies: r-r-utils@2.13.0 r-msnbase@2.34.1 r-biocviews@1.76.0 r-biocmanager@1.30.25
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
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-rnu34cdf 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rnu34cdf
Licenses: LGPL 2.0+
Synopsis: rnu34cdf
Description:

This package provides a package containing an environment representing the RN_U34.CDF file.

r-regsplice 1.36.0
Propagated dependencies: r-summarizedexperiment@1.38.1 r-s4vectors@0.46.0 r-pbapply@1.7-2 r-limma@3.64.1 r-glmnet@4.1-8 r-edger@4.6.2
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/lmweber/regsplice
Licenses: Expat
Synopsis: L1-regularization based methods for detection of differential splicing
Description:

Statistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.

r-rnamodr-ml 1.24.0
Propagated dependencies: r-s4vectors@0.46.0 r-rnamodr@1.24.0 r-ranger@0.17.0 r-iranges@2.42.0 r-genomicranges@1.60.0 r-biocgenerics@0.54.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/FelixErnst/RNAmodR.ML
Licenses: Artistic License 2.0
Synopsis: Detecting patterns of post-transcriptional modifications using machine learning
Description:

RNAmodR.ML extend the functionality of the RNAmodR package and classical detection strategies towards detection through machine learning models. RNAmodR.ML provides classes, functions and an example workflow to establish a detection stratedy, which can be packaged.

r-ribosomeprofilingqc 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/ribosomeProfilingQC
Licenses: FSDG-compatible
Synopsis: Ribosome Profiling Quality Control
Description:

Ribo-Seq (also named ribosome profiling or footprinting) measures translatome (unlike RNA-Seq, which sequences the transcriptome) by direct quantification of the ribosome-protected fragments (RPFs). This package provides the tools for quality assessment of ribosome profiling. In addition, it can preprocess Ribo-Seq data for subsequent differential analysis.

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