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/_/ /      / / /____\/ /       \ \_\\ \/___/ /
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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.

API method:

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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-bsgenome-celegans-ucsc-ce10 1.4.0
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.Celegans.UCSC.ce10/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Worm
Description:

This package provides full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings objects.

r-interactivedisplay 1.48.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biocgenerics@0.56.0 r-biocmanager@1.30.27 r-category@2.76.0 r-ggplot2@4.0.1 r-gridsvg@1.7-7 r-interactivedisplaybase@1.48.0 r-plyr@1.8.9 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-shiny@1.11.1 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/interactiveDisplay
Licenses: Artistic License 2.0
Build system: r
Synopsis: Package for Shiny web displays of Bioconductor objects
Description:

This package offers interactive Shiny displays for Bioconductor objects. In addition, this package empowers users to develop engaging visualizations and interfaces for working with Bioconductor data.

r-breakpointrdata 1.28.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/daewoooo/breakpointRdata
Licenses: Expat
Build system: r
Synopsis: Strand-seq data for demonstration purposes
Description:

This package is a collection of Strand-seq data. The main purpose is to demonstrate functionalities of the breakpointR package.

r-gcrma 2.82.0
Propagated dependencies: r-affy@1.88.0 r-affyio@1.80.0 r-biobase@2.70.0 r-biocmanager@1.30.27 r-biostrings@2.78.0 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/gcrma/
Licenses: LGPL 2.1+
Build system: r
Synopsis: Background adjustment using sequence information
Description:

Gcrma adjusts for background intensities in Affymetrix array data which include optical noise and non-specific binding (NSB). The main function gcrma converts background adjusted probe intensities to expression measures using the same normalization and summarization methods as a Robust Multiarray Average (RMA). Gcrma uses probe sequence information to estimate probe affinity to NSB. The sequence information is summarized in a more complex way than the simple GC content. Instead, the base types (A, T, G or C) at each position along the probe determine the affinity of each probe. The parameters of the position-specific base contributions to the probe affinity is estimated in an NSB experiment in which only NSB but no gene-specific binding is expected.

r-trna 1.28.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-modstrings@1.26.0 r-s4vectors@0.48.0 r-scales@1.4.0 r-stringr@1.6.0 r-structstrings@1.26.0 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/tRNA
Licenses: GPL 3
Build system: r
Synopsis: Analyzing tRNA sequences and structures
Description:

The tRNA package allows tRNA sequences and structures to be accessed and used for subsetting. In addition, it provides visualization tools to compare feature parameters of multiple tRNA sets and correlate them to additional data. The tRNA package uses GRanges objects as inputs requiring only few additional column data sets.

r-inspect 1.40.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-deseq2@1.50.2 r-desolve@1.40 r-genomicalignments@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-kernsmooth@2.23-26 r-plgem@1.82.0 r-proc@1.19.0.1 r-readxl@1.4.5 r-rootsolve@1.8.2.4 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-shiny@1.11.1 r-summarizedexperiment@1.40.0 r-txdb-mmusculus-ucsc-mm9-knowngene@3.2.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/INSPEcT
Licenses: GPL 2
Build system: r
Synopsis: Analysis of 4sU-seq and RNA-seq time-course data
Description:

INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and assess via modeling the rates that determines changes in mature mRNA levels.

r-ciara 0.1.0
Propagated dependencies: r-biobase@2.70.0 r-ggplot2@4.0.1 r-ggraph@2.2.2 r-magrittr@2.0.4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/package=CIARA
Licenses: Artistic License 2.0
Build system: r
Synopsis: Cluster-independent algorithm for rare cell types identification
Description:

This is a package to support identification of markers of rare cell types by looking at genes whose expression is confined in small regions of the expression space.

r-muscat 1.24.0
Propagated dependencies: r-biocparallel@1.44.0 r-blme@1.0-6 r-complexheatmap@2.26.0 r-data-table@1.17.8 r-deseq2@1.50.2 r-dplyr@1.1.4 r-edger@4.8.0 r-ggplot2@4.0.1 r-glmmtmb@1.1.13 r-ihw@1.38.0 r-limma@3.66.0 r-lme4@1.1-37 r-lmertest@3.1-3 r-matrix@1.7-4 r-matrixstats@1.5.0 r-progress@1.2.3 r-purrr@1.2.0 r-rlang@1.1.6 r-s4vectors@0.48.0 r-scales@1.4.0 r-scater@1.38.0 r-sctransform@0.4.2 r-scuttle@1.20.0 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0 r-variancepartition@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/HelenaLC/muscat
Licenses: GPL 3
Build system: r
Synopsis: Multi-sample multi-group scRNA-seq data analysis tools
Description:

This package muscat provides various methods and visualization tools for DS(differential splicing) analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated "pseudobulk" data, as well as a flexible simulation platform that mimics both single and multi-sample scRNA-seq data.

r-cghbase 1.70.0
Propagated dependencies: r-biobase@2.70.0 r-marray@1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/CGHbase
Licenses: GPL 2+
Build system: r
Synopsis: Base functions and classes for arrayCGH data analysis
Description:

This package contains functions and classes that are needed by the arrayCGH packages.

r-apcomplex 2.76.0
Propagated dependencies: r-graph@1.88.0 r-org-sc-sgd-db@3.22.0 r-rbgl@1.86.0 r-rgraphviz@2.54.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/apComplex
Licenses: LGPL 2.0+
Build system: r
Synopsis: Estimate protein complex membership using AP-MS protein data
Description:

This package provides functions to estimate a bipartite graph of protein complex membership using AP-MS data.

r-bladderbatch 1.48.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/bladderbatch
Licenses: Artistic License 2.0
Build system: r
Synopsis: Bladder gene expression data illustrating batch effects
Description:

This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package.

r-flowmeans 1.70.0
Propagated dependencies: r-biobase@2.70.0 r-feature@1.2.15 r-flowcore@2.22.0 r-rrcov@1.7-7
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/flowMeans
Licenses: Artistic License 2.0
Build system: r
Synopsis: Non-parametric flow cytometry data gating
Description:

This package provides tools to identify cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection.

r-genetclassifier 1.50.0
Propagated dependencies: r-biobase@2.70.0 r-e1071@1.7-16 r-ebarrays@2.74.0 r-minet@3.68.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.cicancer.org
Licenses: GPL 2+
Build system: r
Synopsis: Classify diseases and build gene networks using expression profiles
Description:

This is a comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. It provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.

r-pcamethods 2.2.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-mass@7.3-65 r-rcpp@1.1.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/hredestig/pcamethods
Licenses: GPL 3+
Build system: r
Synopsis: Collection of PCA methods
Description:

This package provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results.

r-mast 1.36.0
Propagated dependencies: r-abind@1.4-8 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-data-table@1.17.8 r-ggplot2@4.0.1 r-matrix@1.7-4 r-plyr@1.8.9 r-progress@1.2.3 r-reshape2@1.4.5 r-s4vectors@0.48.0 r-singlecellexperiment@1.32.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/RGLab/MAST/
Licenses: GPL 2+
Build system: r
Synopsis: Model-based analysis of single cell transcriptomics
Description:

This package provides methods and models for handling zero-inflated single cell assay data.

r-alpsnmr 4.12.0
Propagated dependencies: r-baseline@1.3-7 r-biocparallel@1.44.0 r-cli@3.6.5 r-dplyr@1.1.4 r-fs@1.6.6 r-generics@0.1.4 r-ggplot2@4.0.1 r-glue@1.8.0 r-htmltools@0.5.8.1 r-magrittr@2.0.4 r-matrixstats@1.5.0 r-mixomics@6.34.0 r-pcapp@2.0-5 r-purrr@1.2.0 r-readxl@1.4.5 r-reshape2@1.4.5 r-rlang@1.1.6 r-rmarkdown@2.30 r-scales@1.4.0 r-signal@1.8-1 r-speaq@2.7.0 r-stringr@1.6.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-tidyselect@1.2.1 r-vctrs@0.6.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://sipss.github.io/AlpsNMR/
Licenses: Expat
Build system: r
Synopsis: Automated spectral processing system for NMR
Description:

This package reads Bruker NMR data directories both zipped and unzipped. It provides automated and efficient signal processing for untargeted NMR metabolomics. It is able to interpolate the samples, detect outliers, exclude regions, normalize, detect peaks, align the spectra, integrate peaks, manage metadata and visualize the spectra. After spectra processing, it can apply multivariate analysis on extracted data. Efficient plotting with 1-D data is also available. Basic reading of 1D ACD/Labs exported JDX samples is also available.

r-champdata 2.42.0
Propagated dependencies: r-biocgenerics@0.56.0 r-genomicranges@1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ChAMPdata
Licenses: GPL 3
Build system: r
Synopsis: Data packages for ChAMP package
Description:

This package provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis.

r-greylistchip 1.42.0
Propagated dependencies: r-bsgenome@1.78.0 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-mass@7.3-65 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-seqinfo@1.0.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GreyListChIP
Licenses: Artistic License 2.0
Build system: r
Synopsis: Greylist artefact regions based on ChIP inputs
Description:

This package identifies regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling.

r-pscbs 0.68.0
Propagated dependencies: r-aroma-light@3.40.0 r-dnacopy@1.84.0 r-future@1.68.0 r-matrixstats@1.5.0 r-r-cache@0.17.0 r-r-methodss3@1.8.2 r-r-oo@1.27.1 r-r-utils@2.13.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/HenrikBengtsson/PSCBS
Licenses: GPL 2+
Build system: r
Synopsis: Analysis of parent-specific DNA copy numbers
Description:

This is a package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.

r-enrichplot 1.30.3
Propagated dependencies: r-aplot@0.2.9 r-dose@4.4.0 r-ggfun@0.2.0 r-ggnewscale@0.5.2 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-ggtangle@0.0.8 r-ggtree@4.0.1 r-gosemsim@2.36.0 r-igraph@2.2.1 r-magrittr@2.0.4 r-plyr@1.8.9 r-purrr@1.2.0 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-rlang@1.1.6 r-scatterpie@0.2.6 r-yulab-utils@0.2.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/GuangchuangYu/enrichplot
Licenses: Artistic License 2.0
Build system: r
Synopsis: Visualization of functional enrichment result
Description:

The enrichplot package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analyses. All the visualization methods are developed based on ggplot2 graphics.

r-ihw 1.38.0
Propagated dependencies: r-biocgenerics@0.56.0 r-fdrtool@1.2.18 r-lpsymphony@1.38.0 r-slam@0.1-55
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/IHW
Licenses: Artistic License 2.0
Build system: r
Synopsis: Independent hypothesis weighting
Description:

Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.

r-affy 1.88.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-affyio@1.80.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocmanager@1.30.27 r-preprocesscore@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/affy
Licenses: LGPL 2.0+
Build system: r
Synopsis: Methods for affymetrix oligonucleotide arrays
Description:

This package contains functions for exploratory oligonucleotide array analysis.

r-variantannotation 1.56.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-bsgenome@1.78.0 r-curl@7.0.0 r-dbi@1.2.3 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-matrixgenerics@1.22.0 r-rhtslib@3.6.0 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-summarizedexperiment@1.40.0 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/VariantAnnotation
Licenses: Artistic License 2.0
Build system: r
Synopsis: Package for annotation of genetic variants
Description:

This R package can annotate variants, compute amino acid coding changes and predict coding outcomes.

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Total results: 69112