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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:

GET /api/packages?search=hello&page=1&limit=20

where search is your query, page is a page number and limit is a number of items on a single page. Pagination information (such as a number of pages and etc) is returned in response headers.

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-bisquerna 1.0.5
Propagated dependencies: r-biobase@2.68.0 r-limsolve@1.5.7.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.biorxiv.org/content/10.1101/669911v1
Licenses: GPL 3
Synopsis: Decomposition of bulk expression with single-cell sequencing
Description:

This package provides tools to accurately estimate cell type abundances from heterogeneous bulk expression. A reference-based method utilizes single-cell information to generate a signature matrix and transformation of bulk expression for accurate regression based estimates. A marker-based method utilizes known cell-specific marker genes to measure relative abundances across samples.

r-beaddatapackr 1.60.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BeadDataPackR
Licenses: GPL 2
Synopsis: Compression of Illumina BeadArray data
Description:

This package provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.

r-bayseq 2.42.0
Propagated dependencies: r-abind@1.4-8 r-edger@4.6.2 r-genomicranges@1.60.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/baySeq/
Licenses: GPL 3
Synopsis: Bayesian analysis of differential expression patterns in count data
Description:

This package identifies differential expression in high-throughput count data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.

r-sushi 1.34.0
Propagated dependencies: r-biomart@2.64.0 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+
Synopsis: Tools for visualizing genomics data
Description:

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

r-erma 1.24.1
Propagated dependencies: r-annotationdbi@1.70.0 r-biobase@2.68.0 r-biocgenerics@0.54.0 r-biocparallel@1.42.0 r-genomeinfodb@1.44.0 r-genomicfiles@1.44.1 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-homo-sapiens@1.3.1 r-iranges@2.42.0 r-rtracklayer@1.68.0 r-s4vectors@0.46.0 r-shiny@1.10.0 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/erma
Licenses: Artistic License 2.0
Synopsis: Epigenomic road map adventures
Description:

The epigenomics road map describes locations of epigenetic marks in DNA from a variety of cell types. Of interest are locations of histone modifications, sites of DNA methylation, and regions of accessible chromatin. This package presents a selection of elements of the road map including metadata and outputs of the ChromImpute procedure applied to ENCODE cell lines by Ernst and Kellis.

r-qfeatures 1.18.0
Propagated dependencies: r-annotationfilter@1.32.0 r-biobase@2.68.0 r-biocgenerics@0.54.0 r-igraph@2.1.4 r-iranges@2.42.0 r-lazyeval@0.2.2 r-mscoreutils@1.20.0 r-multiassayexperiment@1.34.0 r-plotly@4.10.4 r-protgenerics@1.40.0 r-reshape2@1.4.4 r-s4vectors@0.46.0 r-summarizedexperiment@1.38.1 r-tidyr@1.3.1 r-tidyselect@1.2.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/RforMassSpectrometry/QFeatures
Licenses: Artistic License 2.0
Synopsis: Quantitative features for mass spectrometry data
Description:

The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.

r-cicero 1.26.0
Propagated dependencies: r-assertthat@0.2.1 r-biobase@2.68.0 r-biocgenerics@0.54.0 r-data-table@1.17.4 r-dplyr@1.1.4 r-fnn@1.1.4.1 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-glasso@1.11 r-gviz@1.52.0 r-igraph@2.1.4 r-iranges@2.42.0 r-matrix@1.7-3 r-monocle@2.36.0 r-plyr@1.8.9 r-reshape2@1.4.4 r-s4vectors@0.46.0 r-stringi@1.8.7 r-stringr@1.5.1 r-tibble@3.2.1 r-tidyr@1.3.1 r-vgam@1.1-13
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/cicero/
Licenses: Expat
Synopsis: Predict cis-co-accessibility from single-cell data
Description:

Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends the monocle package for use in chromatin accessibility data.

r-r4rna 1.36.0
Propagated dependencies: r-biostrings@2.76.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.e-rna.org/r-chie/
Licenses: GPL 3
Synopsis: RNA visualization and analysis
Description:

This package provides a package for RNA basepair analysis, including the visualization of basepairs as arc diagrams for easy comparison and annotation of sequence and structure. Arc diagrams can additionally be projected onto multiple sequence alignments to assess basepair conservation and covariation, with numerical methods for computing statistics for each.

r-sva 3.56.0
Propagated dependencies: r-biocparallel@1.42.0 r-edger@4.6.2 r-genefilter@1.90.0 r-limma@3.64.1 r-matrixstats@1.5.0 r-mgcv@1.9-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/sva
Licenses: Artistic License 2.0
Synopsis: Surrogate variable analysis
Description:

This package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. It also contains functions for identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data like gene expression/RNA sequencing/methylation/brain imaging data that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise.

r-chemmineob 1.46.0
Dependencies: eigen@3.4.0 openbabel@3.1.1
Propagated dependencies: r-bh@1.87.0-1 r-biocgenerics@0.54.0 r-rcpp@1.0.14 r-zlibbioc@1.54.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/girke-lab/ChemmineOB
Licenses: ASL 2.0
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-rqc 1.42.0
Propagated dependencies: r-biocgenerics@0.54.0 r-biocparallel@1.42.0 r-biocstyle@2.36.0 r-biostrings@2.76.0 r-biovizbase@1.56.0 r-genomicalignments@1.44.0 r-genomicfiles@1.44.1 r-ggplot2@3.5.2 r-iranges@2.42.0 r-knitr@1.50 r-markdown@2.0 r-plyr@1.8.9 r-rcpp@1.0.14 r-reshape2@1.4.4 r-rsamtools@2.24.0 r-s4vectors@0.46.0 r-shiny@1.10.0 r-shortread@1.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/labbcb/Rqc
Licenses: GPL 2+
Synopsis: Quality control tool for high-throughput sequencing data
Description:

Rqc is an optimized tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.

r-activepathways 2.0.5
Propagated dependencies: r-data-table@1.17.4 r-ggplot2@3.5.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/web/packages/ActivePathways/
Licenses: GPL 3
Synopsis: Multivariate pathway enrichment analysis
Description:

This package represents an integrative method of analyzing multi omics data that conducts enrichment analysis of annotated gene sets. ActivePathways uses a statistical data fusion approach, rationalizes contributing evidence and highlights associated genes, improving systems-level understanding of cellular organization in health and disease.

r-toast 1.22.0
Propagated dependencies: r-corpcor@1.6.10 r-doparallel@1.0.17 r-epidish@2.24.0 r-ggally@2.2.1 r-ggplot2@3.5.2 r-limma@3.64.1 r-nnls@1.6 r-quadprog@1.5-8 r-summarizedexperiment@1.38.1 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
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.

r-clusterprofiler 4.16.0
Propagated dependencies: r-annotationdbi@1.70.0 r-dose@4.2.0 r-dplyr@1.1.4 r-enrichplot@1.28.2 r-go-db@3.21.0 r-gosemsim@2.34.0 r-gson@0.1.0 r-httr@1.4.7 r-igraph@2.1.4 r-magrittr@2.0.3 r-plyr@1.8.9 r-qvalue@2.40.0 r-rlang@1.1.6 r-tidyr@1.3.1 r-yulab-utils@0.2.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://guangchuangyu.github.io/software/clusterProfiler/
Licenses: Artistic License 2.0
Synopsis: Analysis and visualization of functional profiles for gene clusters
Description:

This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.

r-chipcomp 1.38.0
Propagated dependencies: r-biocgenerics@0.54.0 r-bsgenome-hsapiens-ucsc-hg19@1.4.3 r-bsgenome-mmusculus-ucsc-mm9@1.4.0 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-limma@3.64.1 r-rsamtools@2.24.0 r-rtracklayer@1.68.0 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ChIPComp
Licenses: GPL 3+
Synopsis: Quantitative comparison of multiple ChIP-seq datasets
Description:

ChIPComp implements a statistical method for quantitative comparison of multiple ChIP-seq datasets. It detects differentially bound sharp binding sites across multiple conditions considering matching control in ChIP-seq datasets.

r-hpar 1.50.0
Propagated dependencies: r-experimenthub@2.16.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/hpar/
Licenses: Artistic License 2.0
Synopsis: Human Protein Atlas in R
Description:

This package provides a simple interface to and data from the Human Protein Atlas project.

r-summarizedexperiment 1.38.1
Propagated dependencies: r-biobase@2.68.0 r-biocgenerics@0.54.0 r-delayedarray@0.34.1 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-matrix@1.7-3 r-matrixgenerics@1.20.0 r-s4arrays@1.8.0 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/SummarizedExperiment
Licenses: Artistic License 2.0
Synopsis: Container for representing genomic ranges by sample
Description:

The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.

r-omicade4 1.48.0
Propagated dependencies: r-ade4@1.7-23 r-biobase@2.68.0 r-made4@1.82.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/omicade4
Licenses: GPL 2
Synopsis: Multiple co-inertia analysis of omics datasets
Description:

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

r-spatialexperiment 1.18.1
Propagated dependencies: r-biocfilecache@2.16.0 r-biocgenerics@0.54.0 r-magick@2.8.6 r-rjson@0.2.23 r-s4vectors@0.46.0 r-singlecellexperiment@1.30.1 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/drighelli/SpatialExperiment
Licenses: GPL 3
Synopsis: S4 class for spatially resolved -omics data
Description:

This package defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform.

r-codedepends 0.6.6
Propagated dependencies: r-codetools@0.2-20 r-graph@1.86.0 r-xml@3.99-0.18
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/web/packages/CodeDepends
Licenses: GPL 2+ GPL 3+
Synopsis: Analysis of R code for reproducible research and code comprehension
Description:

This package provides tools for analyzing R expressions or blocks of code and determining the dependencies between them. It focuses on R scripts, but can be used on the bodies of functions. There are many facilities including the ability to summarize or get a high-level view of code, determining dependencies between variables, code improvement suggestions.

r-degreport 1.44.0
Propagated dependencies: r-biobase@2.68.0 r-biocgenerics@0.54.0 r-broom@1.0.8 r-circlize@0.4.16 r-cluster@2.1.8.1 r-complexheatmap@2.24.0 r-consensusclusterplus@1.72.0 r-cowplot@1.1.3 r-dendextend@1.19.0 r-deseq2@1.48.1 r-dplyr@1.1.4 r-edger@4.6.2 r-ggdendro@0.2.0 r-ggplot2@3.5.2 r-ggrepel@0.9.6 r-knitr@1.50 r-logging@0.10-108 r-magrittr@2.0.3 r-psych@2.5.3 r-rcolorbrewer@1.1-3 r-reshape@0.8.9 r-rlang@1.1.6 r-s4vectors@0.46.0 r-scales@1.4.0 r-stringi@1.8.7 r-stringr@1.5.1 r-summarizedexperiment@1.38.1 r-tibble@3.2.1 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://lpantano.github.io/DEGreport/
Licenses: Expat
Synopsis: Report of DEG analysis
Description:

This is a package for creating na HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.

r-tricycle 1.16.0
Propagated dependencies: r-annotationdbi@1.70.0 r-circular@0.5-1 r-dplyr@1.1.4 r-genomicranges@1.60.0 r-ggnewscale@0.5.1 r-ggplot2@3.5.2 r-iranges@2.42.0 r-rcolorbrewer@1.1-3 r-s4vectors@0.46.0 r-scater@1.36.0 r-scattermore@1.2 r-singlecellexperiment@1.30.1 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/hansenlab/tricycle
Licenses: GPL 3
Synopsis: Transferable representation and inference of cell cycle
Description:

The package contains functions to infer and visualize cell cycle process using Single-cell RNA-Seq data. It exploits the idea of transfer learning, projecting new data to the previous learned biologically interpretable space. The tricycle provides a pre-learned cell cycle space, which could be used to infer cell cycle time of human and mouse single cell samples. In addition, it also offer functions to visualize cell cycle time on different embeddings and functions to build new reference.

r-siggenes 1.82.0
Propagated dependencies: r-biobase@2.68.0 r-multtest@2.64.0 r-scrime@1.3.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/siggenes/
Licenses: LGPL 2.0+
Synopsis: Multiple testing using SAM and Efron's empirical Bayes approaches
Description:

This package provides tools for the identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).

r-bioccasestudies 1.52.0
Propagated dependencies: r-biobase@2.68.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BiocCaseStudies
Licenses: Artistic License 2.0
Synopsis: Support for the case studies monograph
Description:

This package provides software and data to support the case studies monograph.

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Total results: 45109