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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-shortread 1.68.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biostrings@2.78.0 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-hwriter@1.3.2.1 r-iranges@2.44.0 r-lattice@0.22-7 r-latticeextra@0.6-31 r-pwalign@1.6.0 r-rhtslib@3.6.0 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ShortRead
Licenses: Artistic License 2.0
Build system: r
Synopsis: FASTQ input and manipulation tools
Description:

This package implements sampling, iteration, and input of FASTQ files. It includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

r-reactomepa 1.54.0
Propagated dependencies: r-annotationdbi@1.72.0 r-dose@4.4.0 r-enrichplot@1.30.3 r-ggplot2@4.0.1 r-ggraph@2.2.2 r-graphite@1.56.0 r-gson@0.1.0 r-igraph@2.2.1 r-reactome-db@1.94.0 r-yulab-utils@0.2.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://guangchuangyu.github.io/software/ReactomePA
Licenses: GPL 2
Build system: r
Synopsis: Reactome pathway analysis
Description:

This package provides functions for pathway analysis based on the REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.

r-tcgautils 1.30.1
Propagated dependencies: r-annotationdbi@1.72.0 r-biocbaseutils@1.12.0 r-biocgenerics@0.56.0 r-genomeinfodb@1.46.0 r-genomicdatacommons@1.34.1 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-multiassayexperiment@1.36.1 r-raggedexperiment@1.34.0 r-rvest@1.0.5 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-xml2@1.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/TCGAutils
Licenses: Artistic License 2.0
Build system: r
Synopsis: TCGA utility functions for data management
Description:

This package provides a suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable. Exported functions include those that import data from flat files into Bioconductor objects, convert row annotations, and identifier translation via the GDC API.

r-scaledmatrix 1.18.0
Propagated dependencies: r-delayedarray@0.36.0 r-matrix@1.7-4 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/LTLA/ScaledMatrix
Licenses: GPL 3
Build system: r
Synopsis: Create a DelayedMatrix of scaled and centered values
Description:

This package provides delayed computation of a matrix of scaled and centered values. The result is equivalent to using the scale function but avoids explicit realization of a dense matrix during block processing. This permits greater efficiency in common operations, most notably matrix multiplication.

r-mlinterfaces 1.90.0
Propagated dependencies: r-annotate@1.88.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-cluster@2.1.8.1 r-fpc@2.2-13 r-gbm@2.2.2 r-gdata@3.0.1 r-genefilter@1.92.0 r-ggvis@0.4.9 r-hwriter@1.3.2.1 r-magrittr@2.0.4 r-mass@7.3-65 r-mlbench@2.1-6 r-pls@2.8-5 r-rcolorbrewer@1.1-3 r-rcpp@1.1.0 r-rpart@4.1.24 r-sfsmisc@1.1-23 r-shiny@1.11.1 r-summarizedexperiment@1.40.0 r-threejs@0.3.4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MLInterfaces/
Licenses: LGPL 2.1+
Build system: r
Synopsis: Interfaces to R machine learning procedures
Description:

This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.

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-basilisk 1.22.0
Propagated dependencies: r-dir-expiry@1.18.0 r-reticulate@1.44.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/basilisk
Licenses: GPL 3
Build system: r
Synopsis: Freeze Python dependencies inside Bioconductor packages
Description:

This package installs a self-contained Conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to enable smooth interoperability of multiple Python environments in a single R session.

r-jaspar2020 0.99.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://jaspar.elixir.no/
Licenses: GPL 2
Build system: r
Synopsis: Data package for JASPAR database (version 2020)
Description:

Data package for JASPAR2020. To explore these databases, utilize the TFBSTools package (version 1.23.1 or higher).

r-polyester 1.39.0
Propagated dependencies: r-biostrings@2.78.0 r-iranges@2.44.0 r-limma@3.66.0 r-logspline@2.1.22 r-s4vectors@0.48.0 r-zlibbioc@1.54.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/polyester
Licenses: Artistic License 2.0
Build system: r
Synopsis: Simulate RNA-seq reads
Description:

The polyester package simulates RNA-seq reads from differential expression experiments with replicates. The reads can then be aligned and used to perform comparisons of methods for differential expression.

r-biocsingular 1.26.1
Propagated dependencies: r-assorthead@1.4.0 r-beachmat@2.26.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-delayedarray@0.36.0 r-irlba@2.3.5.1 r-matrix@1.7-4 r-rcpp@1.1.0 r-rsvd@1.0.5 r-s4vectors@0.48.0 r-scaledmatrix@1.18.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/LTLA/BiocSingular
Licenses: GPL 3
Build system: r
Synopsis: Singular value decomposition for Bioconductor packages
Description:

This package implements exact and approximate methods for singular value decomposition and principal components analysis, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Where possible, parallelization is achieved using the BiocParallel framework.

r-atsnp 1.26.0
Propagated dependencies: r-biocfilecache@3.0.0 r-biocparallel@1.44.0 r-bsgenome@1.78.0 r-data-table@1.17.8 r-ggplot2@4.0.1 r-lifecycle@1.0.4 r-motifstack@1.54.0 r-rappdirs@0.3.3 r-rcpp@1.1.0 r-testthat@3.3.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/sunyoungshin/atSNP
Licenses: GPL 2
Build system: r
Synopsis: Affinity test for identifying regulatory single nucleotide polymorphisms
Description:

The atSNP package performs affinity tests of motif matches with the SNP (single nucleotide polymorphism) or the reference genomes and SNP-led changes in motif matches.

r-adductdata 1.26.0
Propagated dependencies: r-annotationhub@4.0.0 r-experimenthub@3.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/adductData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Data from untargeted mass spectrometry of modifications to Cys34
Description:

This package contains data from untargeted mass spectrometry (MS) of modifications to oxidized cysteine (Cys) 34 in human serum albumin (HSA).

r-cpp11bigwig 0.1.2
Dependencies: curl@8.6.0 zlib@1.3.1
Propagated dependencies: r-cpp11@0.5.2 r-genomicranges@1.62.0 r-iranges@2.44.0 r-tibble@3.3.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://rnabioco.github.io/cpp11bigwig/
Licenses: Expat
Build system: r
Synopsis: Read bigWig and bigBed files
Description:

Read bigWig and bigBed files using libBigWig. This package provides lightweight access to the binary bigWig and bigBed formats developed by the UCSC Genome Browser group.

r-flowcore 2.22.0
Propagated dependencies: r-bh@1.87.0-1 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-cpp11@0.5.2 r-cytolib@2.22.0 r-matrixstats@1.5.0 r-rcpp@1.1.0 r-rprotobuflib@2.22.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/flowCore
Licenses: Artistic License 2.0
Build system: r
Synopsis: Basic structures for flow cytometry data
Description:

This package provides S4 data structures and basic functions to deal with flow cytometry data.

r-illuminahumanmethylation450kanno-ilmn12-hg19 0.6.1
Propagated dependencies: r-minfi@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation for Illumina's 450k methylation arrays
Description:

This package provides manifests and annotation for Illumina's 450k array 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-seqarray 1.50.0
Propagated dependencies: r-biostrings@2.78.0 r-digest@0.6.39 r-gdsfmt@1.46.0 r-genomicranges@1.62.0 r-iranges@2.44.0 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/zhengxwen/SeqArray
Licenses: GPL 3
Build system: r
Synopsis: Data management of large-scale whole-genome sequence variant calls
Description:

This package supports data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.

r-watermelon 2.16.0
Propagated dependencies: r-biobase@2.70.0 r-illuminahumanmethylation450kanno-ilmn12-hg19@0.6.1 r-illuminaio@0.52.0 r-limma@3.66.0 r-lumi@2.62.0 r-matrixstats@1.5.0 r-methylumi@2.56.0 r-roc@1.86.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/wateRmelon/
Licenses: GPL 3
Build system: r
Synopsis: Illumina 450 methylation array normalization and metrics
Description:

The standard index of DNA methylation (beta) is computed from methylated and unmethylated signal intensities. Betas calculated from raw signal intensities perform well, but using 11 methylomic datasets we demonstrate that quantile normalization methods produce marked improvement. The commonly used procedure of normalizing betas is inferior to the separate normalization of M and U, and it is also advantageous to normalize Type I and Type II assays separately. This package provides 15 flavours of betas and three performance metrics, with methods for objects produced by the methylumi and minfi packages.

r-bsgenome-mmusculus-ucsc-mm10 1.4.3
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Mouse
Description:

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored in Biostrings objects.

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-minfidata 0.56.0
Propagated dependencies: r-illuminahumanmethylation450kanno-ilmn12-hg19@0.6.1 r-illuminahumanmethylation450kmanifest@0.4.0 r-minfi@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/minfiData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Example data for the Illumina Methylation 450k array
Description:

This package provides data from 6 samples across 2 groups from 450k methylation arrays.

r-adamgui 1.26.0
Propagated dependencies: r-adam@1.26.0 r-colorramps@2.3.4 r-data-table@1.17.8 r-dplyr@1.1.4 r-dt@0.34.0 r-ggplot2@4.0.1 r-ggpubr@0.6.2 r-ggrepel@0.9.6 r-ggsignif@0.6.4 r-go-db@3.22.0 r-gridextra@2.3 r-knitr@1.50 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-shiny@1.11.1 r-shinyjs@2.1.0 r-stringi@1.8.7 r-stringr@1.6.0 r-testthat@3.3.0 r-varhandle@2.0.6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ADAMgui/
Licenses: GPL 2+
Build system: r
Synopsis: GUI for gene activity and diversity analysis
Description:

This package ADAMgui is a graphical user interface (GUI) for the ADAM package. The ADAMgui package provides two shiny-based applications that allows the user to study the output of the ADAM package files through different plots. It's possible, for example, to choose a specific group of functionally associated genes (GFAG) and observe the gene expression behavior with the plots created with the GFAGtargetUi function. Features such as differential expression and fold change can be easily seen with aid of the plots made with the GFAGpathUi function.

r-dir-expiry 1.18.0
Propagated dependencies: r-filelock@1.0.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/dir.expiry
Licenses: GPL 3
Build system: r
Synopsis: Managing expiration for cache directories
Description:

This package implements an expiration system for access to versioned directories. Directories that have not been accessed by a registered function within a certain time frame are deleted. This aims to reduce disk usage by eliminating obsolete caches generated by old versions of packages.

r-ancombc 2.12.0
Propagated dependencies: r-cvxr@1.0-15 r-desctools@0.99.60 r-doparallel@1.0.17 r-dorng@1.8.6.2 r-energy@1.7-12 r-foreach@1.5.2 r-gtools@3.9.5 r-hmisc@5.2-4 r-lme4@1.1-37 r-lmertest@3.1-3 r-mass@7.3-65 r-matrix@1.7-4 r-multcomp@1.4-29 r-nloptr@2.2.1 r-rdpack@2.6.4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/FrederickHuangLin/ANCOMBC
Licenses: Artistic License 2.0
Build system: r
Synopsis: Analysis of compositions of microbiomes with bias correction
Description:

ANCOMBC is a package containing differential abundance (DA) and correlation analyses for microbiome data. Specifically, the package includes Analysis of Compositions of Microbiomes with Bias Correction(ANCOM-BC) and Analysis of Composition of Microbiomes (ANCOM) for DA analysis, and Sparse Estimation of Correlations among Microbiomes (SECOM) for correlation analysis. Microbiome data are typically subject to two sources of biases: unequal sampling fractions (sample-specific biases) and differential sequencing efficiencies (taxon-specific biases). Methodologies included in the ANCOMBC package were designed to correct these biases and construct statistically consistent estimators.

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