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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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If you'd like to join our channel webring send a patch to ~whereiseveryone/toys@lists.sr.ht adding your channel as an entry in channels.scm.


r-a4core 1.58.0
Propagated dependencies: r-biobase@2.70.0 r-glmnet@4.1-10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/a4Core
Licenses: GPL 3
Build system: r
Synopsis: Automated Affymetrix array analysis core package
Description:

This is the core package for the automated analysis of Affymetrix arrays.

r-biotmledata 1.34.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/biotmleData
Licenses: Expat
Build system: r
Synopsis: Example experimental microarray data set for the "biotmle" R package
Description:

This package provides microarray data (from the Illumina Ref-8 BeadChips platform) and phenotype-level data from an epidemiological investigation of benzene exposure, packaged using SummarizedExperiemnt, for use as an example with the biotmle R package.

r-bsgenome-mmusculus-ucsc-mm9 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.Mmusculus.UCSC.mm9/
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 (mm9, July 2007) and stored in Biostrings objects.

r-samr 3.0
Propagated dependencies: r-gsa@1.03.3 r-impute@1.84.0 r-matrixstats@1.5.0 r-openxlsx@4.2.8.1 r-shiny@1.11.1 r-shinyfiles@0.9.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://statweb.stanford.edu/~tibs/SAM/
Licenses: LGPL 3+
Build system: r
Synopsis: Significance analysis of Microarrays
Description:

This is a package for significance analysis of Microarrays for differential expression analysis, RNAseq data and related problems.

r-bader 1.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BADER
Licenses: GPL 2
Build system: r
Synopsis: Bayesian analysis of differential expression in RNA sequencing data
Description:

The BADER package is intended for the analysis of RNA sequencing data. The algorithm fits a Bayesian hierarchical model for RNA sequencing count data. BADER returns the posterior probability of differential expression for each gene between two groups A and B. The joint posterior distribution of the variables in the model can be returned in the form of posterior samples, which can be used for further down-stream analyses such as gene set enrichment.

r-motifbreakr 2.24.0
Propagated dependencies: r-biocfilecache@3.0.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biomart@2.66.0 r-biostrings@2.78.0 r-bsgenome@1.78.0 r-bsicons@0.1.2 r-bslib@0.9.0 r-dt@0.34.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-gviz@1.54.0 r-iranges@2.44.0 r-matrixstats@1.5.0 r-motifdb@1.52.0 r-motifstack@1.54.0 r-pwalign@1.6.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-shiny@1.11.1 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-tfmpvalue@0.0.9 r-variantannotation@1.56.0 r-vroom@1.6.6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/motifbreakR/
Licenses: GPL 2+
Build system: r
Synopsis: Predicting disruptiveness of single nucleotide polymorphisms
Description:

This package allows biologists to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. This package gives a choice of algorithms for interrogation of genomes with motifs from public sources:

  1. a weighted-sum probability matrix;

  2. log-probabilities;

  3. weighted by relative entropy.

This package can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor.

r-motifstack 1.54.0
Propagated dependencies: r-ade4@1.7-23 r-biostrings@2.78.0 r-ggplot2@4.0.1 r-htmlwidgets@1.6.4 r-tfbstools@1.48.0 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/motifStack/
Licenses: GPL 2+
Build system: r
Synopsis: Plot stacked logos for DNA, RNA and amino acid sequences
Description:

The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motifs and amino acid sequence motifs. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.

r-baynorm 1.28.0
Propagated dependencies: r-bb@2019.10-1 r-biocparallel@1.44.0 r-dosnow@1.0.20 r-fitdistrplus@1.2-4 r-foreach@1.5.2 r-iterators@1.0.14 r-locfit@1.5-9.12 r-mass@7.3-65 r-matrix@1.7-4 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1 r-rcppprogress@0.4.2 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/WT215/bayNorm
Licenses: GPL 2+
Build system: r
Synopsis: Single-cell RNA sequencing data normalization
Description:

The bayNorm package is used for normalizing single-cell RNA-seq data. The main function is bayNorm, which is a wrapper function for gene specific prior parameter estimation and normalization. The input is a matrix of scRNA-seq data with rows different genes and columns different cells. The output is either point estimates from posterior (2D array) or samples from posterior (3D array).

r-bsgenome-hsapiens-ncbi-grch38 1.3.1000
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.NCBI.GRCh38.html
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Homo sapiens (GRCh38)
Description:

This package provides full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.

r-progeny 1.32.0
Propagated dependencies: r-biobase@2.70.0 r-decoupler@2.16.0 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-gridextra@2.3 r-reshape2@1.4.5 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/saezlab/progeny
Licenses: ASL 2.0
Build system: r
Synopsis: Pathway responsive gene activity inference
Description:

This package provides a function to infer pathway activity from gene expression. It contains the linear model inferred in the publication "Perturbation-response genes reveal signaling footprints in cancer gene expression".

r-beclear 2.26.0
Propagated dependencies: r-abind@1.4-8 r-biocparallel@1.44.0 r-data-table@1.17.8 r-dixontest@1.0.4 r-futile-logger@1.4.3 r-ids@1.0.1 r-matrix@1.7-4 r-rcpp@1.1.0 r-rdpack@2.6.4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/uds-helms/BEclear
Licenses: GPL 3
Build system: r
Synopsis: Correction of batch effects in DNA methylation data
Description:

This package provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

r-activedriverwgs 1.2.0
Propagated dependencies: r-biostrings@2.78.0 r-bsgenome@1.78.0 r-bsgenome-hsapiens-ucsc-hg19@1.4.3 r-bsgenome-hsapiens-ucsc-hg38@1.4.5 r-bsgenome-mmusculus-ucsc-mm9@1.4.0 r-bsgenome-mmusculus-ucsc-mm10@1.4.3 r-genomeinfodb@1.46.0 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://cran.r-project.org/web/packages/ActiveDriverWGS/
Licenses: GPL 3
Build system: r
Synopsis: Driver discovery tool for cancer whole genomes
Description:

This package provides a method for finding an enrichment of cancer simple somatic mutations (SNVs and Indels) in functional elements across the human genome. ActiveDriverWGS detects coding and noncoding driver elements using whole genome sequencing data.

r-r3cseq 1.56.0
Propagated dependencies: r-biostrings@2.78.0 r-data-table@1.17.8 r-genomicranges@1.62.0 r-iranges@2.44.0 r-qvalue@2.42.0 r-rcolorbrewer@1.1-3 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-seqinfo@1.0.0 r-sqldf@0.4-11 r-vgam@1.1-13
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://r3cseq.genereg.net/Site/index.html
Licenses: GPL 3
Build system: r
Synopsis: Analysis of Chromosome conformation capture and Next-generation sequencing
Description:

This package is used for the analysis of long-range chromatin interactions from 3C-seq assay.

r-ggbio 1.58.0
Propagated dependencies: r-annotationdbi@1.72.0 r-annotationfilter@1.34.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-biovizbase@1.58.0 r-bsgenome@1.78.0 r-ensembldb@2.34.0 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-gridextra@2.3 r-gtable@0.3.6 r-hmisc@5.2-4 r-iranges@2.44.0 r-organismdbi@1.52.0 r-reshape2@1.4.5 r-rlang@1.1.6 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-scales@1.4.0 r-seqinfo@1.0.0 r-summarizedexperiment@1.40.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://www.tengfei.name/ggbio/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Visualization tools for genomic data
Description:

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

r-illuminahumanmethylationepicv2anno-20a1-hg38 1.0.0
Propagated dependencies: r-minfi@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation for Illumina's EPIC v2.0 methylation arrays
Description:

This is an annotation package for Illumina's EPIC v2.0 methylation arrays. The version 2 covers more than 935K CpG sites in the human genome hg38. It is an update of the original EPIC v1.0 array (i.e., the 850K methylation array).

r-minfidataepic 1.36.0
Propagated dependencies: r-illuminahumanmethylationepicanno-ilm10b2-hg19@0.6.0 r-illuminahumanmethylationepicmanifest@0.3.0 r-minfi@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/minfiDataEPIC
Licenses: Artistic License 2.0
Build system: r
Synopsis: Example data for the Illumina Methylation EPIC array
Description:

This package provides data from 3 technical replicates of the cell line GM12878 from the EPIC methylation array.

r-acde 1.40.0
Propagated dependencies: r-boot@1.3-32
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/acde
Licenses: GPL 3
Build system: r
Synopsis: Identification of differentially expressed genes with artificial components
Description:

This package provides a multivariate inferential analysis method for detecting differentially expressed genes in gene expression data. It uses artificial components, close to the data's principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR).

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-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-bumphunter 1.52.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biocgenerics@0.56.0 r-dorng@1.8.6.2 r-foreach@1.5.2 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-iterators@1.0.14 r-limma@3.66.0 r-locfit@1.5-9.12 r-matrixstats@1.5.0 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/ririzarr/bumphunter
Licenses: Artistic License 2.0
Build system: r
Synopsis: Find bumps in genomic data
Description:

This package provides tools for finding bumps in genomic data in order to identify differentially methylated regions in epigenetic epidemiology studies.

r-chemmineob 1.48.0
Dependencies: eigen@3.4.0 openbabel@3.1.1 zlib@1.3.1
Propagated dependencies: r-bh@1.87.0-1 r-biocgenerics@0.56.0 r-rcpp@1.1.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/girke-lab/ChemmineOB
Licenses: ASL 2.0
Build system: r
Synopsis: R interface to a subset of OpenBabel functionalities
Description:

ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is a free cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.

r-sushi 1.34.0
Propagated dependencies: r-biomart@2.66.0 r-zoo@1.8-14
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Sushi
Licenses: GPL 2+
Build system: r
Synopsis: Tools for visualizing genomics data
Description:

This package provides flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures.

r-toast 1.24.0
Propagated dependencies: r-corpcor@1.6.10 r-doparallel@1.0.17 r-epidish@2.26.0 r-ggally@2.4.0 r-ggplot2@4.0.1 r-limma@3.66.0 r-nnls@1.6 r-quadprog@1.5-8 r-summarizedexperiment@1.40.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/TOAST
Licenses: GPL 2
Build system: r
Synopsis: Tools for the analysis of heterogeneous tissues
Description:

This package is devoted to analyzing high-throughput data (e.g. gene expression microarray, DNA methylation microarray, RNA-seq) from complex tissues. Current functionalities include

  1. detect cell-type specific or cross-cell type differential signals

  2. tree-based differential analysis

  3. improve variable selection in reference-free deconvolution

  4. partial reference-free deconvolution with prior knowledge.

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Total results: 68658