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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-fastseg 1.56.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioinf.jku.at/software/fastseg/index.html
Licenses: LGPL 2.0+
Build system: r
Synopsis: Fast segmentation algorithm for genetic sequencing data
Description:

Fastseg implements a very fast and efficient segmentation algorithm. It can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data.

r-org-dm-eg-db 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/org.Dm.eg.db/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Genome wide annotation for Fly
Description:

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model fruit fly Drosophila melanogaster.

r-genomeinfodbdata 1.2.15
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GenomeInfoDbData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Species and taxonomy ID look up tables for GenomeInfoDb
Description:

This package contains data for mapping between NCBI taxonomy ID and species. It is used by functions in the GenomeInfoDb package.

r-dama 1.82.0
Propagated dependencies: r-mass@7.3-65
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/release/bioc/html/daMA.html
Licenses: GPL 2+
Build system: r
Synopsis: Efficient design and analysis of factorial two-colour microarray data
Description:

This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data.

r-aneufinderdata 1.38.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AneuFinderData/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Data package for @code{AneuFinder}
Description:

This package contains whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package.

r-genomicstate 0.99.17
Propagated dependencies: r-annotationdbi@1.72.0 r-annotationhub@4.0.0 r-bumphunter@1.52.0 r-derfinder@1.44.0 r-genomicfeatures@1.62.0 r-iranges@2.44.0 r-org-hs-eg-db@3.22.0 r-rtracklayer@1.70.0 r-seqinfo@1.0.0 r-txdbmaker@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/LieberInstitute/GenomicState
Licenses: Artistic License 2.0
Build system: r
Synopsis: Build and access GenomicState objects
Description:

This package contains functions for building GenomicState objects from different annotation sources such as Gencode. It also provides access to these files at JHPCE.

r-txdb-dmelanogaster-ucsc-dm3-ensgene 3.2.2
Propagated dependencies: r-annotationdbi@1.72.0 r-genomicfeatures@1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm3.ensGene
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for TxDb object(s)
Description:

This package exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

r-ggm 2.5.2
Propagated dependencies: r-biocmanager@1.30.27 r-graph@1.88.0 r-igraph@2.2.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/package=ggm
Licenses: GPL 2+
Build system: r
Synopsis: Functions for graphical Markov models
Description:

This package provides functions and datasets for maximum likelihood fitting of some classes of graphical Markov models.

r-rnbeads 2.28.0
Dependencies: kentutils@302.0.0
Propagated dependencies: r-biocgenerics@0.56.0 r-cluster@2.1.8.1 r-ff@4.5.2 r-fields@17.1 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-gplots@3.2.0 r-gridextra@2.3 r-illuminaio@0.52.0 r-iranges@2.44.0 r-limma@3.66.0 r-mass@7.3-65 r-matrixstats@1.5.0 r-methylumi@2.56.0 r-plyr@1.8.9 r-reshape2@1.4.5 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/RnBeads
Licenses: GPL 3
Build system: r
Synopsis: RnBeads
Description:

RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.

r-monocle3 1.3.7-1.98402ed
Propagated dependencies: r-assertthat@0.2.1 r-batchelor@1.26.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-delayedarray@0.36.0 r-delayedmatrixstats@1.32.0 r-digest@0.6.39 r-dplyr@1.1.4 r-future@1.68.0 r-ggplot2@4.0.1 r-ggrastr@1.0.2 r-ggrepel@0.9.6 r-grr@0.9.5 r-hdf5array@1.38.0 r-igraph@2.2.1 r-irlba@2.3.5.1 r-leidenbase@0.1.35 r-limma@3.66.0 r-lme4@1.1-37 r-lmtest@0.9-40 r-mass@7.3-65 r-matrix@1.7-4 r-openssl@2.3.4 r-pbapply@1.7-4 r-pbmcapply@1.5.1 r-pheatmap@1.0.13 r-plotly@4.11.0 r-plyr@1.8.9 r-proxy@0.4-27 r-pscl@1.5.9 r-purrr@1.2.0 r-rann@2.6.2 r-rcolorbrewer@1.1-3 r-rcpp@1.1.0 r-rcppannoy@0.0.22 r-rcpphnsw@0.6.0 r-reshape2@1.4.5 r-rhpcblasctl@0.23-42 r-rsample@1.3.1 r-rtsne@0.17 r-s4vectors@0.48.0 r-sf@1.0-23 r-shiny@1.11.1 r-singlecellexperiment@1.32.0 r-slam@0.1-55 r-spdep@1.4-1 r-speedglm@0.3-5 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-uwot@0.2.4 r-viridis@0.6.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/cole-trapnell-lab/monocle3
Licenses: Expat
Build system: r
Synopsis: Analysis toolkit for single-cell RNA-Seq data
Description:

Monocle 3 performs clustering, differential expression and trajectory analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle 3 also performs differential expression analysis, clustering, visualization, and other useful tasks on single-cell expression data. It is designed to work with RNA-Seq data, but could be used with other types as well.

r-leukemiaseset 1.46.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/leukemiasEset
Licenses: GPL 2+
Build system: r
Synopsis: Leukemia's microarray gene expression data (expressionSet)
Description:

This package provides an expressionSet containing gene expression data from 60 bone marrow samples of patients with one of the four main types of leukemia (ALL, AML, CLL, CML) or non-leukemia.

r-bamsignals 1.42.0
Propagated dependencies: r-biocgenerics@0.56.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rcpp@1.1.0 r-rhtslib@3.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/bamsignals
Licenses: GPL 2+
Build system: r
Synopsis: Extract read count signals from bam files
Description:

This package efficiently obtains count vectors from indexed bam files. It counts the number of nucleotide sequence reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

r-saturn 1.18.0
Propagated dependencies: r-biocparallel@1.44.0 r-boot@1.3-32 r-ggplot2@4.0.1 r-limma@3.66.0 r-locfdr@1.1-8 r-matrix@1.7-4 r-pbapply@1.7-4 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/statOmics/satuRn
Licenses: Artistic License 2.0
Build system: r
Synopsis: Analysis of differential transcript usage for scRNA-seq applications
Description:

satuRn provides a framework for performing differential transcript usage analyses. The package consists of three main functions. The first function, fitDTU, fits quasi-binomial generalized linear models that model transcript usage in different groups of interest. The second function, testDTU, tests for differential usage of transcripts between groups of interest. Finally, plotDTU visualizes the usage profiles of transcripts in groups of interest.

r-biobroom 1.42.0
Propagated dependencies: r-biobase@2.70.0 r-broom@1.0.10 r-dplyr@1.1.4 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/StoreyLab/biobroom
Licenses: LGPL 3+
Build system: r
Synopsis: Turn Bioconductor objects into tidy data frames
Description:

This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.

r-geneplotter 1.88.0
Propagated dependencies: r-annotate@1.88.0 r-annotationdbi@1.72.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-lattice@0.22-7 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/geneplotter
Licenses: Artistic License 2.0
Build system: r
Synopsis: Graphics functions for genomic data
Description:

This package provides functions for plotting genomic data.

r-edger 4.8.0
Propagated dependencies: r-limma@3.66.0 r-locfit@1.5-9.12
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioinf.wehi.edu.au/edgeR
Licenses: GPL 2+
Build system: r
Synopsis: EdgeR does empirical analysis of digital gene expression data
Description:

This package can do differential expression analysis of RNA-seq expression profiles with biological replication. It implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. It be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE.

r-derfinder 1.44.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-bumphunter@1.52.0 r-derfinderhelper@1.44.0 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicfeatures@1.62.0 r-genomicfiles@1.46.0 r-genomicranges@1.62.0 r-hmisc@5.2-4 r-iranges@2.44.0 r-qvalue@2.42.0 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/lcolladotor/derfinder
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation-agnostic differential expression analysis of RNA-seq data
Description:

This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package:

  1. single base-level F-statistics and

  2. DER identification at the expressed regions-level.

The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.

r-organism-dplyr 1.37.1
Propagated dependencies: r-annotationdbi@1.72.0 r-annotationfilter@1.34.0 r-biocfilecache@3.0.0 r-dbi@1.2.3 r-dbplyr@2.5.1 r-dplyr@1.1.4 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rlang@1.1.6 r-rsqlite@2.4.4 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-tibble@3.3.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Organism.dplyr
Licenses: Artistic License 2.0
Build system: r
Synopsis: Dplyr-based access to Bioconductor annotation resources
Description:

This package provides an alternative interface to Bioconductor annotation resources, in particular the gene identifier mapping functionality of the org packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the TxDb packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

r-assorthead 1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/LTLA/assorthead
Licenses: Expat
Build system: r
Synopsis: Assorted header-only C++ libraries
Description:

This package vendors an assortment of useful header-only C++ libraries. Bioconductor packages can use these libraries in their own C++ code by LinkingTo this package without introducing any additional dependencies. The use of a central repository avoids duplicate vendoring of libraries across multiple R packages, and enables better coordination of version updates across cohorts of interdependent C++ libraries.

r-metapod 1.18.0
Propagated dependencies: r-rcpp@1.1.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/metapod
Licenses: GPL 3
Build system: r
Synopsis: Meta-analyses on p-values of differential analyses
Description:

This package implements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in ChIP-seq, exons in RNA-seq) or for corresponding tests across separate analyses (e.g., replicated comparisons, effect of different treatment conditions). Support is provided for handling log-transformed input p-values, missing values and weighting where appropriate.

r-txdb-hsapiens-ucsc-hg19-knowngene 3.22.1
Propagated dependencies: r-annotationdbi@1.72.0 r-genomicfeatures@1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for human genome in TxDb format
Description:

This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg19 genome and based on the "knownGene" track. The database is exposed as a TxDb object.

r-speaq 2.7.0
Propagated dependencies: r-cluster@2.1.8.1 r-data-table@1.17.8 r-dosnow@1.0.20 r-foreach@1.5.2 r-ggplot2@4.0.1 r-gridextra@2.3 r-impute@1.84.0 r-massspecwavelet@1.76.0 r-missforest@1.6.1 r-reshape2@1.4.5 r-rfast@2.1.5.2 r-rvest@1.0.5 r-xml2@1.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/package=speaq
Licenses: ASL 2.0
Build system: r
Synopsis: Tools for nuclear magnetic resonance spectra alignment
Description:

This package aims to make NMR spectroscopy data analysis as easy as possible. It only requires a small set of functions to perform an entire analysis. Speaq offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed with any number of statistical tools either included in speaq or available elsewhere on CRAN.

r-interactivedisplaybase 1.48.0
Propagated dependencies: r-biocgenerics@0.56.0 r-dt@0.34.0 r-shiny@1.11.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/interactiveDisplayBase
Licenses: Artistic License 2.0
Build system: r
Synopsis: Base package for web displays of Bioconductor objects
Description:

This package contains the basic methods needed to generate interactive Shiny-based display methods for Bioconductor objects.

r-rgadem 2.55.0
Propagated dependencies: r-biostrings@2.78.0 r-bsgenome@1.78.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-seqlogo@1.76.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/rGADEM/
Licenses: Artistic License 2.0
Build system: r
Synopsis: De novo sequence motif discovery
Description:

rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data.

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Total results: 69112