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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-a4 1.58.0
Propagated dependencies: r-a4base@1.58.0 r-a4classif@1.58.0 r-a4core@1.58.0 r-a4preproc@1.58.0 r-a4reporting@1.58.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/a4/
Licenses: GPL 3
Build system: r
Synopsis: Automated Affymetrix array analysis umbrella package
Description:

This package provides a software suite for the automated analysis of Affymetrix arrays.

r-prolocdata 1.48.0
Propagated dependencies: r-biobase@2.70.0 r-msnbase@2.36.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/lgatto/pRolocdata
Licenses: GPL 2
Build system: r
Synopsis: Data accompanying the pRoloc package
Description:

This package provides mass-spectrometry based spatial proteomics data sets and protein complex separation data. It also contains the time course expression experiment from Mulvey et al. (2015).

r-imputelcmd 2.1
Propagated dependencies: r-impute@1.84.0 r-norm@1.0-11.1 r-pcamethods@2.2.0 r-tmvtnorm@1.7
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/package=imputeLCMD
Licenses: GPL 2+
Build system: r
Synopsis: Collection of methods for left-censored missing data imputation
Description:

This package provides a collection of functions for left-censored missing data imputation. Left-censoring is a special case of missing not at random (MNAR) mechanism that generates non-responses in proteomics experiments. The package also contains functions to artificially generate peptide/protein expression data (log-transformed) as random draws from a multivariate Gaussian distribution as well as a function to generate missing data (both randomly and non-randomly). For comparison reasons, the package also contains several wrapper functions for the imputation of non-responses that are missing at random.

r-xina 1.28.0
Propagated dependencies: r-alluvial@0.1-2 r-ggplot2@4.0.1 r-gridextra@2.3 r-igraph@2.2.1 r-mclust@6.1.2 r-plyr@1.8.9 r-stringdb@2.22.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://git.bioconductor.org/packages/XINA
Licenses: GPL 3
Build system: r
Synopsis: Identifying proteins that exhibit similar patterns
Description:

The aim of XINA is to determine which proteins exhibit similar patterns within and across experimental conditions, since proteins with co-abundance patterns may have common molecular functions. XINA imports multiple datasets, tags dataset in silico, and combines the data for subsequent subgrouping into multiple clusters. The result is a single output depicting the variation across all conditions. XINA not only extracts coabundance profiles within and across experiments, but also incorporates protein-protein interaction databases and integrative resources such as Kyoto encyclopedia of genes and genomes (KEGG) to infer interactors and molecular functions, respectively, and produces intuitive graphical outputs.

r-omicade4 1.50.0
Propagated dependencies: r-ade4@1.7-23 r-biobase@2.70.0 r-made4@1.84.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/omicade4
Licenses: GPL 2
Build system: r
Synopsis: Multiple co-inertia analysis of omics datasets
Description:

This package performs multiple co-inertia analysis of omics datasets.

r-aldex2 1.42.0
Propagated dependencies: r-biocparallel@1.44.0 r-directlabels@2025.6.24 r-genomicranges@1.62.0 r-iranges@2.44.0 r-lattice@0.22-7 r-latticeextra@0.6-31 r-multtest@2.66.0 r-rfast@2.1.5.2 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0 r-zcompositions@1.5.0-5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ggloor/ALDEx_bioc
Licenses: AGPL 3+ GPL 2+ GPL 3
Build system: r
Synopsis: Analysis of differential abundance taking sample variation into account
Description:

This package provides a differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch's t-test, a Kruskal-Wallis test, a generalized linear model, or a correlation test. All tests report p-values and Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs.

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.

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-deconvr 1.16.0
Propagated dependencies: r-assertthat@0.2.1 r-biocgenerics@0.56.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-e1071@1.7-16 r-foreach@1.5.2 r-genomicranges@1.62.0 r-iranges@2.44.0 r-magrittr@2.0.4 r-mass@7.3-65 r-matrixstats@1.5.0 r-methylkit@1.36.0 r-minfi@1.56.0 r-nnls@1.6 r-quadprog@1.5-8 r-rsq@2.7 r-s4vectors@0.48.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/BIMSBbioinfo/deconvR
Licenses: Artistic License 2.0
Build system: r
Synopsis: Simulation and deconvolution of omic profiles
Description:

This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types. The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally, we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.

r-flowclust 3.48.0
Dependencies: gsl@2.8
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-flowcore@2.22.0 r-graph@1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/flowClust
Licenses: Artistic License 2.0
Build system: r
Synopsis: Clustering for flow cytometry
Description:

This package provides robust model-based clustering using a t-mixture model with Box-Cox transformation.

r-awst 1.18.0
Propagated dependencies: r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/drisso/awst
Licenses: Expat
Build system: r
Synopsis: Asymmetric within-sample transformation
Description:

This package awst (Asymmetric Within-Sample Transformation) that regularizes RNA-seq read counts and reduces the effect of noise on the classification of samples. AWST comprises two main steps: standardization and smoothing. These steps transform gene expression data to reduce the noise of the lowly expressed features, which suffer from background effects and low signal-to-noise ratio, and the influence of the highly expressed features, which may be the result of amplification bias and other experimental artifacts.

r-biscuiteer 1.24.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biscuiteerdata@1.24.0 r-bsseq@1.46.0 r-data-table@1.17.8 r-delayedmatrixstats@1.32.0 r-dmrseq@1.30.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-gtools@3.9.5 r-hdf5array@1.38.0 r-homo-sapiens@1.3.1 r-impute@1.84.0 r-iranges@2.44.0 r-matrix@1.7-4 r-matrixstats@1.5.0 r-mus-musculus@1.3.1 r-qdnaseq@1.46.0 r-qualv@0.3-5 r-r-utils@2.13.0 r-readr@2.1.6 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/trichelab/biscuiteer
Licenses: GPL 3
Build system: r
Synopsis: Convenience functions for the Biscuit package
Description:

This package provides a test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.

r-bhc 1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BHC/
Licenses: GPL 3
Build system: r
Synopsis: Bayesian hierarchical clustering
Description:

The method implemented in this package performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data. This version also includes a randomised algorithm which is more efficient for larger data sets.

r-mdqc 1.72.0
Propagated dependencies: r-cluster@2.1.8.1 r-mass@7.3-65
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/mdqc
Licenses: LGPL 2.0+
Build system: r
Synopsis: Mahalanobis distance quality control for microarrays
Description:

MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array's quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.

r-bgeecall 1.26.0
Propagated dependencies: kallisto@0.50.1 r-annotationdbi@1.72.0 r-biostrings@2.78.0 r-curl@7.0.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-genomicfeatures@1.62.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-jsonlite@2.0.0 r-rcurl@1.98-1.17 r-readr@2.1.6 r-rhdf5@2.54.0 r-rslurm@0.6.2 r-rsqlite@2.4.4 r-rtracklayer@1.70.0 r-scales@1.4.0 r-sjmisc@2.8.11 r-sjmisc@2.8.11 r-spatstat-univar@3.1-5 r-stringr@1.6.0 r-txdbmaker@1.6.0 r-tximport@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/BgeeDB/BgeeCall
Licenses: GPL 3
Build system: r
Synopsis: RNA-Seq present/absent gene expression calls generation
Description:

BgeeCall allows generating present/absent gene expression calls without using an arbitrary cutoff like TPM<1. Calls are generated based on reference intergenic sequences. These sequences are generated based on expression of all RNA-Seq libraries of each species integrated in Bgee.

r-singler 2.12.0
Propagated dependencies: r-assorthead@1.4.0 r-beachmat@2.26.0 r-biocneighbors@2.4.0 r-biocparallel@1.44.0 r-delayedarray@0.36.0 r-delayedmatrixstats@1.32.0 r-matrix@1.7-4 r-rcpp@1.1.0 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/LTLA/SingleR
Licenses: GPL 3
Build system: r
Synopsis: Reference-based single-cell RNA-seq annotation
Description:

This package performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.

r-a4base 1.58.0
Propagated dependencies: r-a4core@1.58.0 r-a4preproc@1.58.0 r-annaffy@1.82.0 r-biobase@2.70.0 r-genefilter@1.92.0 r-glmnet@4.1-10 r-gplots@3.2.0 r-limma@3.66.0 r-mpm@1.0-23 r-multtest@2.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/a4Base/
Licenses: GPL 3
Build system: r
Synopsis: Automated Affymetrix array analysis base package
Description:

This package provides basic features for the automated analysis of Affymetrix arrays.

r-pathview 1.50.0
Propagated dependencies: r-annotationdbi@1.72.0 r-graph@1.88.0 r-kegggraph@1.70.0 r-keggrest@1.50.0 r-org-hs-eg-db@3.22.0 r-png@0.1-8 r-rgraphviz@2.54.0 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://pathview.uncc.edu/
Licenses: GPL 3+
Build system: r
Synopsis: Tool set for pathway based data integration and visualization
Description:

r-pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. This package automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, r-pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.

r-delayedmatrixstats 1.32.0
Propagated dependencies: r-delayedarray@0.36.0 r-iranges@2.44.0 r-matrix@1.7-4 r-matrixgenerics@1.22.0 r-s4vectors@0.48.0 r-sparsearray@1.10.2 r-sparsematrixstats@1.22.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/PeteHaitch/DelayedMatrixStats
Licenses: Expat
Build system: r
Synopsis: Functions that apply to rows and columns of DelayedMatrix objects
Description:

This package provides a port of the matrixStats API for use with DelayedMatrix objects from the DelayedArray package. It contains high-performing functions operating on rows and columns of DelayedMatrix objects, e.g. colMedians, rowMedians, colRanks, rowRanks, colSds, and rowSds. Functions are optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.

r-vsn 3.78.0
Propagated dependencies: r-affy@1.88.0 r-biobase@2.70.0 r-ggplot2@4.0.1 r-lattice@0.22-7 r-limma@3.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/release/bioc/html/vsn.html
Licenses: Artistic License 2.0
Build system: r
Synopsis: Variance stabilization and calibration for microarray data
Description:

The package implements a method for normalising microarray intensities, and works for single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.

r-bsgenome-drerio-ucsc-danrer11 1.4.2
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer11
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Danio rerio (UCSC version danRer11)
Description:

This package provides full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer11, May 2017) and stored in Biostrings objects.

r-rhisat2 1.26.0
Propagated dependencies: r-genomicranges@1.62.0 r-sgseq@1.44.0 r-txdbmaker@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/fmicompbio/Rhisat2
Licenses: GPL 3
Build system: r
Synopsis: R Wrapper for HISAT2 sequence aligner
Description:

This package provides an R interface to the HISAT2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.

r-biocneighbors 2.4.0
Propagated dependencies: r-assorthead@1.4.0 r-rcpp@1.1.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BiocNeighbors
Licenses: GPL 3
Build system: r
Synopsis: Nearest Neighbor Detection for Bioconductor packages
Description:

This package implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. The exact algorithm is implemented using pre-clustering with the k-means algorithm. Functions are also provided to search for all neighbors within a given distance. Parallelization is achieved for all methods using the BiocParallel framework.

r-triform 1.29.0
Propagated dependencies: r-biocgenerics@0.56.0 r-iranges@2.44.0 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/triform/
Licenses: GPL 2
Build system: r
Synopsis: Find enriched regions in transcription factor ChIP-sequencing data
Description:

The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.

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