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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-spp 1.16.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-bh@1.87.0-1 r-catools@1.18.3 r-rcpp@1.1.0 r-rsamtools@2.26.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/web/packages/spp/
Licenses: GPL 2
Build system: r
Synopsis: ChIP-Seq processing pipeline
Description:

This package provides tools for analysis of ChIP-seq and other functional sequencing data.

r-icens 1.82.0
Propagated dependencies: r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Icens
Licenses: Artistic License 2.0
Build system: r
Synopsis: NPMLE for censored and truncated data
Description:

This package provides many functions for computing the nonparametric maximum likelihood estimator (NPMLE) for censored and truncated data.

r-restfulr 0.0.16
Propagated dependencies: r-rcurl@1.98-1.17 r-rjson@0.2.23 r-s4vectors@0.48.0 r-xml@3.99-0.20 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/package=restfulr
Licenses: Artistic License 2.0
Build system: r
Synopsis: R interface to RESTful web services
Description:

This package models a RESTful service as if it were a nested R list.

r-pfamanalyzer 1.10.0
Propagated dependencies: r-dplyr@1.1.4 r-magrittr@2.0.4 r-readr@2.1.6 r-stringr@1.6.0 r-tibble@3.3.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/pfamAnalyzeR
Licenses: Expat
Build system: r
Synopsis: Identification of domain isotypes in pfam data
Description:

This R package enables the user to read pfam predictions into R. Most human protein domains exist as multiple distinct variants termed domain isotypes. This R package enables the identification and classification of such domain isotypes from pfam data.

r-methylaiddata 1.42.0
Propagated dependencies: r-methylaid@1.44.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MethylAidData
Licenses: GPL 2+
Build system: r
Synopsis: MethylAid-summarized data for 2800 Illumina 450k array samples and 2620 EPIC array samples
Description:

This package provides a data package containing summarized Illumina 450k array data on 2800 samples and summarized EPIC data for 2620 samples. The data can be use as a background data set in the interactive application.

r-airpart 1.18.0
Propagated dependencies: r-apeglm@1.32.0 r-clue@0.3-66 r-complexheatmap@2.26.0 r-dplyr@1.1.4 r-dynamictreecut@1.63-1 r-emdbook@1.3.14 r-forestplot@3.1.7 r-ggplot2@4.0.1 r-lpsolve@5.6.23 r-matrixstats@1.5.0 r-mclust@6.1.2 r-pbapply@1.7-4 r-plyr@1.8.9 r-rcolorbrewer@1.1-3 r-rlang@1.1.6 r-s4vectors@0.48.0 r-scater@1.38.0 r-singlecellexperiment@1.32.0 r-smurf@1.1.8 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/airpart
Licenses: GPL 2
Build system: r
Synopsis: Differential cell-type-specific allelic imbalance
Description:

The airpart package identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of a generalized fused lasso with binomial observations of allelic counts to partition cell types by their allelic imbalance. Alternatively, a nonparametric method for partitioning cell types is offered. The package includes a number of visualizations and quality control functions for examining single cell allelic imbalance datasets.

r-annotationdbi 1.72.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-dbi@1.2.3 r-iranges@2.44.0 r-keggrest@1.50.0 r-rsqlite@2.4.4 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AnnotationDbi
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation database interface
Description:

This package provides user interface and database connection code for annotation data packages using SQLite data storage.

r-preprocesscore 1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/bmbolstad/preprocessCore
Licenses: LGPL 2.0+
Build system: r
Synopsis: Collection of pre-processing functions
Description:

This package provides a library of core pre-processing and normalization routines.

r-isoformswitchanalyzer 2.10.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biostrings@2.78.0 r-bsgenome@1.78.0 r-dbi@1.2.3 r-dexseq@1.56.0 r-dplyr@1.1.4 r-edger@4.8.0 r-futile-logger@1.4.3 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-gridextra@2.3 r-iranges@2.44.0 r-limma@3.66.0 r-magrittr@2.0.4 r-pfamanalyzer@1.10.0 r-plyr@1.8.9 r-pwalign@1.6.0 r-rcolorbrewer@1.1-3 r-rcurl@1.98-1.17 r-readr@2.1.6 r-reshape2@1.4.5 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-saturn@1.18.0 r-seqinfo@1.0.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-sva@3.58.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-tximeta@1.28.0 r-tximport@1.38.1 r-venndiagram@1.7.3 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/IsoformSwitchAnalyzeR/
Licenses: GPL 2+
Build system: r
Synopsis: Analyze alternative splicing in RNA-seq data
Description:

This is a package for the analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.

r-birewire 3.41.0
Propagated dependencies: r-igraph@2.2.1 r-matrix@1.7-4 r-rtsne@0.17 r-slam@0.1-55
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/release/bioc/html/BiRewire.html
Licenses: GPL 3
Build system: r
Synopsis: Tools for randomization of bipartite graphs
Description:

This package provides functions for bipartite network rewiring through N consecutive switching steps and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. It includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections.

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-s4arrays 1.10.0
Propagated dependencies: r-abind@1.4-8 r-biocgenerics@0.56.0 r-iranges@2.44.0 r-matrix@1.7-4 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/S4Arrays
Licenses: Artistic License 2.0
Build system: r
Synopsis: Foundation of array-like containers in Bioconductor
Description:

The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides:

  1. low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and

  2. a framework that facilitates block processing of array-like objects (typically on-disk objects).

r-xcms 4.8.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-data-table@1.17.8 r-iranges@2.44.0 r-lattice@0.22-7 r-massspecwavelet@1.76.0 r-metabocoreutils@1.18.1 r-mscoreutils@1.21.0 r-msexperiment@1.12.0 r-msfeatures@1.18.0 r-msnbase@2.36.0 r-mzr@2.44.0 r-progress@1.2.3 r-protgenerics@1.42.0 r-rcolorbrewer@1.1-3 r-s4vectors@0.48.0 r-spectra@1.20.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/xcms/
Licenses: GPL 2+
Build system: r
Synopsis: LC/MS and GC/MS mass spectrometry data analysis
Description:

This package provides a framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. It imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses data for high-throughput, untargeted analyte profiling.

r-txdb-mmusculus-ucsc-mm9-knowngene 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.Mmusculus.UCSC.mm9.knownGene/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for mouse genome in TxDb format
Description:

This package provides an annotation database of Mouse genome data. It is derived from the UCSC mm9 genome and based on the "knownGene" track. The database is exposed as a TxDb object.

r-biodb 1.18.0
Propagated dependencies: r-chk@0.10.0 r-fscache@1.0.5 r-jsonlite@2.0.0 r-lgr@0.5.0 r-lifecycle@1.0.4 r-openssl@2.3.4 r-plyr@1.8.9 r-progress@1.2.3 r-r6@2.6.1 r-rappdirs@0.3.3 r-rcpp@1.1.0 r-rsqlite@2.4.4 r-sched@1.0.3 r-sqlq@1.0.1 r-stringr@1.6.0 r-testthat@3.3.0 r-withr@3.0.2 r-xml@3.99-0.20 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/biodb
Licenses: AGPL 3+
Build system: r
Synopsis: Library for connecting to chemical and biological databases
Description:

The biodb package provides access to standard remote chemical and biological databases (ChEBI, KEGG, HMDB, ...), as well as to in-house local database files (CSV, SQLite), with easy retrieval of entries, access to web services, search of compounds by mass and/or name, and mass spectra matching for LCMS and MSMS. Its architecture as a development framework facilitates the development of new database connectors for local projects or inside separate published packages.

r-mixomics 6.34.0
Propagated dependencies: r-biocparallel@1.44.0 r-corpcor@1.6.10 r-dplyr@1.1.4 r-ellipse@0.5.0 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-gridextra@2.3 r-gsignal@0.3-7 r-igraph@2.2.1 r-lattice@0.22-7 r-mass@7.3-65 r-matrixstats@1.5.0 r-rarpack@0.11-0 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-rgl@1.3.31 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://www.mixOmics.org
Licenses: GPL 2+
Build system: r
Synopsis: Multivariate methods for exploration of biological datasets
Description:

mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data.

r-polyphen-hsapiens-dbsnp131 1.0.2
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/PolyPhen.Hsapiens.dbSNP131
Licenses: Artistic License 2.0
Build system: r
Synopsis: PolyPhen predictions for Homo sapiens dbSNP build 131
Description:

This package provides a database of PolyPhen predictions for Homo sapiens dbSNP build 131.

r-flowviz 1.74.0
Propagated dependencies: r-biobase@2.70.0 r-flowcore@2.22.0 r-hexbin@1.28.5 r-idpmisc@1.1.21 r-kernsmooth@2.23-26 r-lattice@0.22-7 r-latticeextra@0.6-31 r-mass@7.3-65 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/flowViz/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Visualization for flow cytometry
Description:

This package provides visualization tools for flow cytometry data.

r-iclusterplus 1.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/iClusterPlus/
Licenses: GPL 2+
Build system: r
Synopsis: Integrative clustering of multi-type genomic data
Description:

iClusterPlus is developed for integrative clustering analysis of multi-type genomic data and is an enhanced version of iCluster proposed and developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise from the experiments where biological samples (e.g. tumor samples) are analyzed by multiple techniques, for instance, array comparative genomic hybridization (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so on. In the iClusterPlus model, binary observations such as somatic mutation are modeled as Binomial processes; categorical observations such as copy number states are realizations of Multinomial random variables; counts are modeled as Poisson random processes; and continuous measures are modeled by Gaussian distributions.

r-universalmotif 1.28.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-mass@7.3-65 r-matrixgenerics@1.22.0 r-rcpp@1.1.0 r-rcppthread@2.2.0 r-rlang@1.1.6 r-s4vectors@0.48.0 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/universalmotif/
Licenses: GPL 3
Build system: r
Synopsis: Specific structures importer, modifier, and exporter for R
Description:

This package allows importing most common specific structure (motif) types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.

r-a4reporting 1.58.0
Propagated dependencies: r-xtable@1.8-4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/a4Reporting/
Licenses: GPL 3
Build system: r
Synopsis: Automated Affymetrix array analysis reporting package
Description:

This is a package for the automated analysis of Affymetrix arrays. It provides reporting features.

r-systempiperdata 2.14.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-jsonlite@2.0.0 r-remotes@2.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/tgirke/systemPipeRdata
Licenses: Artistic License 2.0
Build system: r
Synopsis: Workflow templates and sample data
Description:

systemPipeRdata complements the systemPipeR workflow management system (WMS) by offering a collection of pre-designed data analysis workflow templates. These templates are easily accessible and can be readily loaded onto a user's system with a single command. Once loaded, the WMS can immediately utilize these templates for efficient end-to-end analysis, serving a wide range of data analysis needs.

r-illuminahumanmethylationepicanno-ilm10b4-hg19 0.6.0
Propagated dependencies: r-minfi@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://doi.org/doi:10.18129/B9.bioc.IlluminaHumanMethylationEPICanno.ilm10b4.hg19
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation for Illumina's EPIC methylation arrays
Description:

This is an annotation package for Illumina's EPIC methylation arrays.

r-dnacopy 1.84.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/DNAcopy
Licenses: GPL 2+
Build system: r
Synopsis: DNA copy number data analysis
Description:

This package implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.

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