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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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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.

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r-cyp450cdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cyp450cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: cyp450cdf
Description:

This package provides a package containing an environment representing the CYP450.CDF file.

r-chromscape 1.20.0
Propagated dependencies: r-viridis@0.6.5 r-umap@0.2.10.0 r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-stringdist@0.9.15 r-singlecellexperiment@1.32.0 r-shinywidgets@0.9.0 r-shinyjs@2.1.0 r-shinyhelper@0.3.2 r-shinyfiles@0.9.3 r-shinydashboardplus@2.0.6 r-shinydashboard@0.7.3 r-shinycssloaders@1.1.0 r-shiny@1.11.1 r-scran@1.38.0 r-scater@1.38.0 r-s4vectors@0.48.0 r-rtsne@0.17 r-rtracklayer@1.70.0 r-rsamtools@2.26.0 r-rlist@0.4.6.2 r-rcpp@1.1.0 r-qualv@0.3-5 r-qs@0.27.3 r-plotly@4.11.0 r-msigdbr@25.1.1 r-matrixtests@0.2.3.1 r-matrix@1.7-4 r-kableextra@1.4.0 r-jsonlite@2.0.0 r-irlba@2.3.5.1 r-iranges@2.44.0 r-gridextra@2.3 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-gggenes@0.5.1 r-genomicranges@1.62.0 r-fs@1.6.6 r-forcats@1.0.1 r-edger@4.8.0 r-dt@0.34.0 r-dplyr@1.1.4 r-delayedarray@0.36.0 r-coop@0.6-3 r-consensusclusterplus@1.74.0 r-colourpicker@1.3.0 r-colorramps@2.3.4 r-biocparallel@1.44.0 r-batchelor@1.26.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/vallotlab/ChromSCape
Licenses: GPL 3
Build system: r
Synopsis: Analysis of single-cell epigenomics datasets with a Shiny App
Description:

ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.

r-cydar 1.34.0
Propagated dependencies: r-viridis@0.6.5 r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-shiny@1.11.1 r-s4vectors@0.48.0 r-rcpp@1.1.0 r-flowcore@2.22.0 r-biocparallel@1.44.0 r-biocneighbors@2.4.0 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cydar
Licenses: GPL 3
Build system: r
Synopsis: Using Mass Cytometry for Differential Abundance Analyses
Description:

Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.

r-cytopipelinegui 1.8.0
Propagated dependencies: r-shiny@1.11.1 r-plotly@4.11.0 r-ggplot2@4.0.1 r-flowcore@2.22.0 r-cytopipeline@1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://uclouvain-cbio.github.io/CytoPipelineGUI
Licenses: GPL 3
Build system: r
Synopsis: GUI's for visualization of flow cytometry data analysis pipelines
Description:

This package is the companion of the `CytoPipeline` package. It provides GUI's (shiny apps) for the visualization of flow cytometry data analysis pipelines that are run with `CytoPipeline`. Two shiny applications are provided, i.e. an interactive flow frame assessment and comparison tool and an interactive scale transformations visualization and adjustment tool.

r-compcoder 1.46.0
Propagated dependencies: r-vioplot@0.5.1 r-stringr@1.6.0 r-sm@2.2-6.0 r-shinydashboard@0.7.3 r-shiny@1.11.1 r-rocr@1.0-11 r-rmarkdown@2.30 r-phylolm@2.6.5 r-modeest@2.4.0 r-matrixstats@1.5.0 r-mass@7.3-65 r-markdown@2.0 r-limma@3.66.0 r-lattice@0.22-7 r-knitr@1.50 r-kernsmooth@2.23-26 r-gtools@3.9.5 r-gplots@3.2.0 r-ggplot2@4.0.1 r-edger@4.8.0 r-catools@1.18.3 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/csoneson/compcodeR
Licenses: GPL 2+
Build system: r
Synopsis: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
Description:

This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data. Finally, it provides convenient interfaces to several packages for performing the differential expression analysis. These can also be used as templates for setting up and running a user-defined differential analysis workflow within the framework of the package.

r-cnorode 1.52.0
Propagated dependencies: r-genalg@0.2.1 r-cellnoptr@1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CNORode
Licenses: GPL 2
Build system: r
Synopsis: ODE add-on to CellNOptR
Description:

Logic based ordinary differential equation (ODE) add-on to CellNOptR.

r-consensus 1.28.0
Propagated dependencies: r-rcolorbrewer@1.1-3 r-matrixstats@1.5.0 r-gplots@3.2.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/consensus
Licenses: Modified BSD
Build system: r
Synopsis: Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
Description:

An implementation of the American Society for Testing and Materials (ASTM) Standard E691 for interlaboratory testing procedures, designed for cross-platform genomic measurements. Given three (3) or more genomic platforms or laboratory protocols, this package provides interlaboratory testing procedures giving per-locus comparisons for sensitivity and precision between platforms.

r-clipper 1.50.0
Propagated dependencies: r-rcpp@1.1.0 r-qpgraph@2.44.0 r-matrix@1.7-4 r-kegggraph@1.70.0 r-igraph@2.2.1 r-grbase@2.0.3 r-graph@1.88.0 r-corpcor@1.6.10 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/clipper
Licenses: AGPL 3
Build system: r
Synopsis: Gene Set Analysis Exploiting Pathway Topology
Description:

This package implements topological gene set analysis using a two-step empirical approach. It exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype.

r-cola 2.16.1
Propagated dependencies: r-xml2@1.5.0 r-skmeans@0.2-19 r-rcpp@1.1.0 r-rcolorbrewer@1.1-3 r-png@0.1-8 r-microbenchmark@1.5.0 r-mclust@6.1.2 r-matrixstats@1.5.0 r-markdown@2.0 r-knitr@1.50 r-irlba@2.3.5.1 r-impute@1.84.0 r-httr@1.4.7 r-globaloptions@0.1.2 r-getoptlong@1.0.5 r-foreach@1.5.2 r-eulerr@7.0.4 r-dorng@1.8.6.2 r-doparallel@1.0.17 r-digest@0.6.39 r-crayon@1.5.3 r-complexheatmap@2.26.0 r-cluster@2.1.8.1 r-clue@0.3-66 r-circlize@0.4.16 r-brew@1.0-10 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/jokergoo/cola
Licenses: Expat
Build system: r
Synopsis: Framework for Consensus Partitioning
Description:

Subgroup classification is a basic task in genomic data analysis, especially for gene expression and DNA methylation data analysis. It can also be used to test the agreement to known clinical annotations, or to test whether there exist significant batch effects. The cola package provides a general framework for subgroup classification by consensus partitioning. It has the following features: 1. It modularizes the consensus partitioning processes that various methods can be easily integrated. 2. It provides rich visualizations for interpreting the results. 3. It allows running multiple methods at the same time and provides functionalities to straightforward compare results. 4. It provides a new method to extract features which are more efficient to separate subgroups. 5. It automatically generates detailed reports for the complete analysis. 6. It allows applying consensus partitioning in a hierarchical manner.

r-clustcomp 1.38.0
Propagated dependencies: r-sm@2.2-6.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/clustComp
Licenses: GPL 2+
Build system: r
Synopsis: Clustering Comparison Package
Description:

clustComp is a package that implements several techniques for the comparison and visualisation of relationships between different clustering results, either flat versus flat or hierarchical versus flat. These relationships among clusters are displayed using a weighted bi-graph, in which the nodes represent the clusters and the edges connect pairs of nodes with non-empty intersection; the weight of each edge is the number of elements in that intersection and is displayed through the edge thickness. The best layout of the bi-graph is provided by the barycentre algorithm, which minimises the weighted number of crossings. In the case of comparing a hierarchical and a non-hierarchical clustering, the dendrogram is pruned at different heights, selected by exploring the tree by depth-first search, starting at the root. Branches are decided to be split according to the value of a scoring function, that can be based either on the aesthetics of the bi-graph or on the mutual information between the hierarchical and the flat clusterings. A mapping between groups of clusters from each side is constructed with a greedy algorithm, and can be additionally visualised.

r-cardinalworkflows 1.42.0
Propagated dependencies: r-cardinal@3.12.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CardinalWorkflows
Licenses: Artistic License 2.0
Build system: r
Synopsis: Datasets and workflows for the Cardinal MSI
Description:

Datasets and workflows for Cardinal: DESI and MALDI examples including pig fetus, cardinal painting, and human RCC.

r-curatedovariandata 1.48.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: http://bcb.dfci.harvard.edu/ovariancancer
Licenses: Artistic License 2.0
Build system: r
Synopsis: Clinically Annotated Data for the Ovarian Cancer Transcriptome
Description:

The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer.

r-chipseqr 1.64.0
Propagated dependencies: r-timsac@1.3.8-4 r-shortread@1.68.0 r-s4vectors@0.48.0 r-iranges@2.44.0 r-hilbertvis@1.68.0 r-genomicranges@1.62.0 r-fbasics@4041.97 r-biostrings@2.78.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/ChIPseqR
Licenses: GPL 2+
Build system: r
Synopsis: Identifying Protein Binding Sites in High-Throughput Sequencing Data
Description:

ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.

r-cllmethylation 1.30.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CLLmethylation
Licenses: LGPL 2.0+
Build system: r
Synopsis: Methylation data of primary CLL samples in PACE project
Description:

The package includes DNA methylation data for the primary Chronic Lymphocytic Leukemia samples included in the Primary Blood Cancer Encyclopedia (PACE) project. Raw data from the 450k DNA methylation arrays is stored in the European Genome-Phenome Archive (EGA) under accession number EGAS0000100174. For more information concerning the project please refer to the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) and R/Bioconductor package BloodCancerMultiOmics2017.

r-cnorfeeder 1.50.0
Propagated dependencies: r-graph@1.88.0 r-cellnoptr@1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CNORfeeder
Licenses: GPL 3
Build system: r
Synopsis: Integration of CellNOptR to add missing links
Description:

This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with links derived from the data via various inference methods and uses information on physical interactions of proteins to guide and validate the integration of links.

r-cosmic-67 1.46.0
Propagated dependencies: r-variantannotation@1.56.0 r-summarizedexperiment@1.40.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/COSMIC.67
Licenses: GPL 3
Build system: r
Synopsis: COSMIC.67
Description:

COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24).

r-cqn 1.56.0
Propagated dependencies: r-quantreg@6.1 r-nor1mix@1.3-3 r-mclust@6.1.2
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cqn
Licenses: Artistic License 2.0
Build system: r
Synopsis: Conditional quantile normalization
Description:

This package provides a normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.

r-cellmapperdata 1.36.0
Propagated dependencies: r-experimenthub@3.0.0 r-cellmapper@1.36.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CellMapperData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Pre-processed data for use with the CellMapper package
Description:

Experiment data package. Contains microarray data from several large expression compendia that have been pre-processed for use with the CellMapper package. This pre-processed data is recommended for routine searches using the CellMapper package.

r-countsimqc 1.28.0
Propagated dependencies: r-tidyr@1.3.1 r-summarizedexperiment@1.40.0 r-rmarkdown@2.30 r-randtests@1.0.2 r-ragg@1.5.0 r-ggplot2@4.0.1 r-genomeinfodbdata@1.2.15 r-genefilter@1.92.0 r-edger@4.8.0 r-dt@0.34.0 r-dplyr@1.1.4 r-deseq2@1.50.2 r-catools@1.18.3
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/csoneson/countsimQC
Licenses: FSDG-compatible
Build system: r
Synopsis: Compare Characteristic Features of Count Data Sets
Description:

countsimQC provides functionality to create a comprehensive report comparing a broad range of characteristics across a collection of count matrices. One important use case is the comparison of one or more synthetic count matrices to a real count matrix, possibly the one underlying the simulations. However, any collection of count matrices can be compared.

r-cadra 1.8.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-reshape2@1.4.5 r-r-cache@0.17.0 r-ppcor@1.1 r-plyr@1.8.9 r-misc3d@0.9-1 r-mass@7.3-65 r-knnmi@1.0 r-gtable@0.3.6 r-gplots@3.2.0 r-ggplot2@4.0.1 r-doparallel@1.0.17
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/montilab/CaDrA/
Licenses: FSDG-compatible
Build system: r
Synopsis: Candidate Driver Analysis
Description:

This package performs both stepwise and backward heuristic search for candidate (epi)genetic drivers based on a binary multi-omics dataset. CaDrA's main objective is to identify features which, together, are significantly skewed or enriched pertaining to a given vector of continuous scores (e.g. sample-specific scores representing a phenotypic readout of interest, such as protein expression, pathway activity, etc.), based on the union occurence (i.e. logical OR) of the events.

r-celaref 1.28.0
Propagated dependencies: r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rlang@1.1.6 r-readr@2.1.6 r-matrix@1.7-4 r-mast@1.36.0 r-magrittr@2.0.4 r-ggplot2@4.0.1 r-dplyr@1.1.4 r-delayedarray@0.36.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/celaref
Licenses: GPL 3
Build system: r
Synopsis: Single-cell RNAseq cell cluster labelling by reference
Description:

After the clustering step of a single-cell RNAseq experiment, this package aims to suggest labels/cell types for the clusters, on the basis of similarity to a reference dataset. It requires a table of read counts per cell per gene, and a list of the cells belonging to each of the clusters, (for both test and reference data).

r-cancerclass 1.54.0
Propagated dependencies: r-biobase@2.70.0 r-binom@1.1-1.1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cancerclass
Licenses: FSDG-compatible
Build system: r
Synopsis: Development and validation of diagnostic tests from high-dimensional molecular data
Description:

The classification protocol starts with a feature selection step and continues with nearest-centroid classification. The accurarcy of the predictor can be evaluated using training and test set validation, leave-one-out cross-validation or in a multiple random validation protocol. Methods for calculation and visualization of continuous prediction scores allow to balance sensitivity and specificity and define a cutoff value according to clinical requirements.

r-clariomsrathttranscriptcluster-db 8.8.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/clariomsrathttranscriptcluster.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix clariomsratht annotation data (chip clariomsrathttranscriptcluster)
Description:

Affymetrix clariomsratht annotation data (chip clariomsrathttranscriptcluster) assembled using data from public repositories.

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Total results: 68658