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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-rfarm 1.22.0
Propagated dependencies: r-xml2@1.5.0 r-stringi@1.8.7 r-s4vectors@0.48.0 r-rvest@1.0.5 r-rsvg@2.7.0 r-magick@2.9.0 r-jsonlite@2.0.0 r-iranges@2.44.0 r-httr@1.4.7 r-data-table@1.17.8 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rfaRm
Licenses: GPL 3
Build system: r
Synopsis: An R interface to the Rfam database
Description:

rfaRm provides a client interface to the Rfam database of RNA families. Data that can be retrieved include RNA families, secondary structure images, covariance models, sequences within each family, alignments leading to the identification of a family and secondary structures in the dot-bracket format.

r-rgug4131a-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/rgug4131a.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Agilent "Rat Genome, Whole" annotation data (chip rgug4131a)
Description:

Agilent "Rat Genome, Whole" annotation data (chip rgug4131a) assembled using data from public repositories.

r-ragene11stprobeset-db 8.8.0
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/ragene11stprobeset.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix ragene11 annotation data (chip ragene11stprobeset)
Description:

Affymetrix ragene11 annotation data (chip ragene11stprobeset) assembled using data from public repositories.

r-ruvnormalizedata 1.30.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RUVnormalizeData
Licenses: GPL 3
Build system: r
Synopsis: Gender data for the RUVnormalize package
Description:

Microarray gene expression data from the study of Vawter et al., 2004.

r-rbiopaxparser 2.50.0
Propagated dependencies: r-xml@3.99-0.20 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/frankkramer-lab/rBiopaxParser
Licenses: GPL 2+
Build system: r
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-rtu34probe 2.18.0
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/rtu34probe
Licenses: LGPL 2.0+
Build system: r
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-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-rscudo 1.26.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-s4vectors@0.48.0 r-igraph@2.2.1 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/Matteo-Ciciani/scudo
Licenses: GPL 3
Build system: r
Synopsis: Signature-based Clustering for Diagnostic Purposes
Description:

SCUDO (Signature-based Clustering for Diagnostic Purposes) is a rank-based method for the analysis of gene expression profiles for diagnostic and classification purposes. It is based on the identification of sample-specific gene signatures composed of the most up- and down-regulated genes for that sample. Starting from gene expression data, functions in this package identify sample-specific gene signatures and use them to build a graph of samples. In this graph samples are joined by edges if they have a similar expression profile, according to a pre-computed similarity matrix. The similarity between the expression profiles of two samples is computed using a method similar to GSEA. The graph of samples can then be used to perform community clustering or to perform supervised classification of samples in a testing set.

r-rae230a-db 3.13.0
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/rae230a.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix RAE230A Array annotation data (chip rae230a)
Description:

Affymetrix Affymetrix RAE230A Array annotation data (chip rae230a) assembled using data from public repositories.

r-rgsea 1.44.0
Propagated dependencies: r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RGSEA
Licenses: FSDG-compatible
Build system: r
Synopsis: Random Gene Set Enrichment Analysis
Description:

Combining bootstrap aggregating and Gene set enrichment analysis (GSEA), RGSEA is a classfication algorithm with high robustness and no over-fitting problem. It performs well especially for the data generated from different exprements.

r-rcm 1.26.0
Propagated dependencies: r-vgam@1.1-13 r-tseries@0.10-58 r-tensor@1.5.1 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-phyloseq@1.54.0 r-nleqslv@3.3.5 r-mass@7.3-65 r-ggplot2@4.0.1 r-edger@4.8.0 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
Build system: r
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-ribosomeprofilingqc 1.22.0
Propagated dependencies: r-xvector@0.50.0 r-txdbmaker@1.6.0 r-seqinfo@1.0.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-ruvseq@1.44.0 r-rtracklayer@1.70.0 r-rsubread@2.24.0 r-rsamtools@2.26.0 r-motifstack@1.54.0 r-iranges@2.44.0 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-ggfittext@0.10.2 r-ggextra@0.11.0 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0 r-genomeinfodb@1.46.0 r-edaseq@2.44.0 r-cluster@2.1.8.1 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocgenerics@0.56.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/ribosomeProfilingQC
Licenses: FSDG-compatible
Build system: r
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.

r-rcgh 1.40.0
Propagated dependencies: r-txdb-hsapiens-ucsc-hg38-knowngene@3.22.0 r-txdb-hsapiens-ucsc-hg19-knowngene@3.22.1 r-txdb-hsapiens-ucsc-hg18-knowngene@3.2.2 r-shiny@1.11.1 r-seqinfo@1.0.0 r-plyr@1.8.9 r-org-hs-eg-db@3.22.0 r-mclust@6.1.2 r-limma@3.66.0 r-lattice@0.22-7 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-dnacopy@1.84.0 r-annotationdbi@1.72.0 r-affy@1.88.0 r-acgh@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/fredcommo/rCGH
Licenses: Artistic License 2.0
Build system: r
Synopsis: Comprehensive Pipeline for Analyzing and Visualizing Array-Based CGH Data
Description:

This package provides a comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools. rCGH also supports custom arrays, provided data complies with the expected format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to profiles segmentation and gene annotations. This package also provides several visualization functions (static or interactive) which facilitate individual profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.

r-rlmm 1.72.0
Propagated dependencies: r-mass@7.3-65
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://www.stat.berkeley.edu/users/nrabbee/RLMM
Licenses: LGPL 2.0+
Build system: r
Synopsis: Genotype Calling Algorithm for Affymetrix SNP Arrays
Description:

This package provides a classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.

r-rhesuscdf 2.18.0
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/rhesuscdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: rhesuscdf
Description:

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

r-rgu34acdf 2.18.0
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/rgu34acdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: rgu34acdf
Description:

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

r-raer 1.8.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rsamtools@2.26.0 r-rhtslib@3.6.0 r-matrix@1.7-4 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0 r-genomeinfodb@1.46.0 r-cli@3.6.5 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://rnabioco.github.io/raer
Licenses: Expat
Build system: r
Synopsis: RNA editing tools in R
Description:

Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.

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-rnbeads-mm9 1.42.0
Propagated dependencies: r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RnBeads.mm9
Licenses: GPL 3
Build system: r
Synopsis: RnBeads.mm9
Description:

Automatically generated RnBeads annotation package for the assembly mm9.

r-rtn 2.34.1
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://dx.doi.org/10.1038/ncomms3464
Licenses: Artistic License 2.0
Build system: r
Synopsis: RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons
Description:

This package provides a transcriptional regulatory network (TRN) consists of a collection of transcription factors (TFs) and the regulated target genes. TFs are regulators that recognize specific DNA sequences and guide the expression of the genome, either activating or repressing the expression the target genes. The set of genes controlled by the same TF forms a regulon. This package provides classes and methods for the reconstruction of TRNs and analysis of regulons.

r-rjmcmcnucleosomes 1.34.0
Dependencies: gsl@2.8
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rcpp@1.1.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-consensusseeker@1.38.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/ArnaudDroitLab/RJMCMCNucleosomes
Licenses: Artistic License 2.0
Build system: r
Synopsis: Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
Description:

This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.

r-rtcga-mutations 20151101.40.0
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.mutations
Licenses: GPL 2
Build system: r
Synopsis: Mutations datasets from The Cancer Genome Atlas Project
Description:

Package provides mutations datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Mutations data format is explained here https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification. There is extra one column with patients barcodes. Data from 2015-11-01 snapshot.

r-rnbeads-mm10 2.18.0
Propagated dependencies: r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RnBeads.mm10
Licenses: GPL 3
Build system: r
Synopsis: RnBeads.mm10
Description:

Automatically generated RnBeads annotation package for the assembly mm10.

r-ragene10stv1probe 2.18.0
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/ragene10stv1probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type ragene10stv1
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 RaGene-1\_0-st-v1\_probe\_tab.

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Total results: 69112