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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-alabaster-base 1.10.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-alabaster-schemas@1.10.0 r-assorthead@1.4.0 r-digest@0.6.39 r-jsonlite@2.0.0 r-jsonvalidate@1.5.0 r-rcpp@1.1.0 r-rhdf5@2.54.0 r-rhdf5lib@1.32.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/alabaster.base
Licenses: Expat
Build system: r
Synopsis: Save Bioconductor objects to file
Description:

This is a package for saving Bioconductor data structures into file artifacts, and loading them back into memory. This is a more robust and portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

r-guitar 2.26.0
Propagated dependencies: r-annotationdbi@1.72.0 r-dplyr@1.1.4 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-knitr@1.50 r-magrittr@2.0.4 r-rtracklayer@1.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Guitar
Licenses: GPL 2
Build system: r
Synopsis: Visualize genomic features
Description:

This package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.

r-sift-hsapiens-dbsnp137 1.0.0
Propagated dependencies: r-annotationdbi@1.72.0 r-rsqlite@2.4.4 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/SIFT.Hsapiens.dbSNP137
Licenses: Artistic License 2.0
Build system: r
Synopsis: PROVEAN/SIFT predictions for Homo sapiens dbSNP build 137
Description:

This package provides a database of PROVEAN/SIFT predictions for Homo sapiens dbSNP build 137.

r-sparsematrixstats 1.22.0
Propagated dependencies: r-matrix@1.7-4 r-matrixgenerics@1.22.0 r-matrixstats@1.5.0 r-rcpp@1.1.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/sparseMatrixStats/
Licenses: Expat
Build system: r
Synopsis: Summary statistics for rows and columns of sparse matrices
Description:

This package provides high performance functions for row and column operations on sparse matrices. Currently, the optimizations are limited to data in the column sparse format.

r-deds 1.60.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/DEDS/
Licenses: LGPL 3+
Build system: r
Synopsis: Differential expression via distance summary for microarray data
Description:

This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.

r-cardelino 1.12.0
Propagated dependencies: r-combinat@0.0-8 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-ggtree@4.0.1 r-matrix@1.7-4 r-matrixstats@1.5.0 r-pheatmap@1.0.13 r-s4vectors@0.48.0 r-snpstats@1.60.0 r-variantannotation@1.56.0 r-vcfr@1.15.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/single-cell-genetics/cardelino
Licenses: GPL 3
Build system: r
Synopsis: Clone identification from single cell data
Description:

This package provides methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used.

r-coverageview 1.48.0
Propagated dependencies: r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/CoverageView/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Coverage visualization package for R
Description:

This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or other experiment types where it is important to have a framework in order to inspect how the coverage distributed across the genome.

r-pepsnmr 1.28.0
Propagated dependencies: r-ggplot2@4.0.1 r-gridextra@2.3 r-matrix@1.7-4 r-matrixstats@1.5.0 r-ptw@1.9-16 r-reshape2@1.4.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ManonMartin/PepsNMR
Licenses: GPL 2
Build system: r
Synopsis: Pre-process 1H-NMR FID signals
Description:

This package provides R functions for common pre-processing steps that are applied on 1H-NMR data. It also provides a function to read the FID signals directly in the Bruker format.

r-matrixgenerics 1.22.0
Propagated dependencies: r-matrixstats@1.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MatrixGenerics
Licenses: Artistic License 2.0
Build system: r
Synopsis: S4 generic summary statistic functions for matrix-like objects
Description:

This package provides S4 generic functions modeled after the matrixStats API for alternative matrix implementations. Packages with alternative matrix implementation can depend on this package and implement the generic functions that are defined here for a useful set of row and column summary statistics. Other package developers can import this package and handle a different matrix implementations without worrying about incompatibilities.

r-chromstardata 1.36.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/chromstaRData/
Licenses: GPL 3
Build system: r
Synopsis: ChIP-seq data for demonstration purposes
Description:

This package provides ChIP-seq data for demonstration purposes in the chromstaR package.

r-beachmat-hdf5 1.8.0
Propagated dependencies: r-assorthead@1.4.0 r-beachmat@2.26.0 r-delayedarray@0.36.0 r-hdf5array@1.38.0 r-rcpp@1.1.0 r-rhdf5lib@1.32.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/beachmat.hdf5
Licenses: GPL 3
Build system: r
Synopsis: beachmat bindings for HDF5-backed matrices
Description:

This package extends beachmat to support initialization of tatami matrices from HDF5-backed arrays. This allows C++ code in downstream packages to directly call the HDF5 C/C++ library to access array data, without the need for block processing via DelayedArray. Some utilities are also provided for direct creation of an in-memory tatami matrix from a HDF5 file.

r-limma 3.66.0
Propagated dependencies: r-statmod@1.5.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioinf.wehi.edu.au/limma
Licenses: GPL 2+
Build system: r
Synopsis: Package for linear models for microarray and RNA-seq data
Description:

This package can be used for the analysis of gene expression studies, especially the use of linear models for analysing designed experiments and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.

r-activepathways 2.0.6
Propagated dependencies: r-data-table@1.17.8 r-ggplot2@4.0.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/web/packages/ActivePathways/
Licenses: GPL 3
Build system: r
Synopsis: Multivariate pathway enrichment analysis
Description:

This package represents an integrative method of analyzing multi omics data that conducts enrichment analysis of annotated gene sets. ActivePathways uses a statistical data fusion approach, rationalizes contributing evidence and highlights associated genes, improving systems-level understanding of cellular organization in health and disease.

r-biocviews 1.78.0
Propagated dependencies: r-biobase@2.70.0 r-biocmanager@1.30.27 r-graph@1.88.0 r-rbgl@1.86.0 r-rcurl@1.98-1.17 r-runit@0.4.33.1 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/biocViews
Licenses: Artistic License 2.0
Build system: r
Synopsis: Bioconductor package categorization helper
Description:

The purpose of biocViews is to create HTML pages that categorize packages in a Bioconductor package repository according to keywords, also known as views, in a controlled vocabulary.

r-affylmgui 1.84.0
Propagated dependencies: r-affy@1.88.0 r-affyio@1.80.0 r-affyplm@1.86.0 r-annotationdbi@1.72.0 r-biocgenerics@0.56.0 r-biocmanager@1.30.27 r-gcrma@2.82.0 r-limma@3.66.0 r-r2html@2.3.4 r-tkrplot@0.0-30 r-xtable@1.8-4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioinf.wehi.edu.au/affylmGUI/
Licenses: GPL 2+
Build system: r
Synopsis: GUI for limma package with Affymetrix microarrays
Description:

This package provides a GUI for analysis of Affymetrix microarray gene expression data using the affy and limma packages.

r-rdisop 1.70.0
Propagated dependencies: r-rcpp@1.1.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/sneumann/Rdisop
Licenses: GPL 2
Build system: r
Synopsis: Decomposition of isotopic patterns
Description:

This is a package for identification of metabolites using high precision mass spectrometry. MS peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.

r-siggenes 1.84.0
Propagated dependencies: r-biobase@2.70.0 r-multtest@2.66.0 r-scrime@1.3.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/siggenes/
Licenses: LGPL 2.0+
Build system: r
Synopsis: Multiple testing using SAM and Efron's empirical Bayes approaches
Description:

This package provides tools for the identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).

r-chemminer 3.62.0
Propagated dependencies: r-base64enc@0.1-3 r-bh@1.87.0-1 r-biocgenerics@0.56.0 r-dbi@1.2.3 r-digest@0.6.39 r-dt@0.34.0 r-ggplot2@4.0.1 r-gridextra@2.3 r-jsonlite@2.0.0 r-png@0.1-8 r-rcpp@1.1.0 r-rcurl@1.98-1.17 r-rjson@0.2.23 r-rsvg@2.7.0 r-stringi@1.8.7
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/girke-lab/ChemmineR
Licenses: Artistic License 2.0
Build system: r
Synopsis: Cheminformatics toolkit for R
Description:

ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. It contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.

r-faahko 1.50.0
Propagated dependencies: r-xcms@4.8.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://dx.doi.org/10.1021/bi0480335
Licenses: LGPL 2.0+
Build system: r
Synopsis: Saghatelian et al. (2004) FAAH knockout LC/MS data
Description:

This package includes positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). It also includes detected peaks in an xcmsSet.

r-quantsmooth 1.76.0
Propagated dependencies: r-quantreg@6.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/quantsmooth
Licenses: GPL 2
Build system: r
Synopsis: Quantile smoothing and genomic visualization of array data
Description:

This package implements quantile smoothing. It contains a dataset used to produce human chromosomal ideograms for plotting purposes and a collection of arrays that contains data of chromosome 14 of 3 colorectal tumors. The package provides functions for painting chromosomal icons, chromosome or chromosomal idiogram and other types of plots. Quantsmooth offers options like converting chromosomal ids to their numeric form, retrieving the human chromosomal length from NCBI data, retrieving regions of interest in a vector of intensities using quantile smoothing, determining cytoband position based on the location of the probe, and other useful tools.

r-sushi 1.34.0
Propagated dependencies: r-biomart@2.66.0 r-zoo@1.8-14
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Sushi
Licenses: GPL 2+
Build system: r
Synopsis: Tools for visualizing genomics data
Description:

This package provides flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures.

r-basic4cseq 1.46.0
Propagated dependencies: r-biostrings@2.78.0 r-bsgenome-ecoli-ncbi-20080805@1.3.1000 r-catools@1.18.3 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-rcircos@1.2.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Basic4Cseq
Licenses: LGPL 3
Build system: r
Synopsis: Analyzing 4C-seq data
Description:

Basic4Cseq is an R package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

r-hybridmtest 1.54.0
Propagated dependencies: r-biobase@2.70.0 r-fdrtool@1.2.18 r-mass@7.3-65 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/HybridMTest
Licenses: GPL 2+
Build system: r
Synopsis: Hybrid multiple testing
Description:

This package performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using EBP estimates obtained by Grenander density estimation. For instance, for 3-group comparison analysis, Hybrid Multiple testing considers EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test of normality as weight. Instead of just using EBPs from F-test only or using H-test only, this methodology combines both types of EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses then the law of total EBPs.

r-ensdb-hsapiens-v79 2.99.0
Propagated dependencies: r-ensembldb@2.34.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/EnsDb.Hsapiens.v79
Licenses: Artistic License 2.0
Build system: r
Synopsis: Ensembl based annotation package
Description:

This package exposes an annotation database generated from Ensembl.

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Total results: 68655