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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-aucell 1.32.0
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-delayedarray@0.36.0 r-delayedmatrixstats@1.32.0 r-gseabase@1.72.0 r-matrix@1.7-4 r-mixtools@2.0.0.1 r-r-utils@2.13.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AUCell/
Licenses: GPL 3
Build system: r
Synopsis: Analysis of gene set activity in single-cell RNA-seq data
Description:

AUCell identifies cells with active gene sets (e.g. signatures, gene modules, etc) in single-cell RNA-seq data. AUCell uses the Area Under the Curve (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.

r-fhtest 1.5.1
Propagated dependencies: r-interval@1.1-1.0 r-kmsurv@0.1-6 r-mass@7.3-65 r-perm@1.0-0.4 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/web/packages/FHtest/
Licenses: GPL 2+
Build system: r
Synopsis: Tests for survival data based on the Fleming-Harrington class
Description:

This package provides functions to compare two or more survival curves with:

  • The Fleming-Harrington test for right-censored data based on permutations and on counting processes.

  • An extension of the Fleming-Harrington test for interval-censored data based on a permutation distribution and on a score vector distribution.

r-scone 1.34.0
Propagated dependencies: r-aroma-light@3.40.0 r-biocparallel@1.44.0 r-boot@1.3-32 r-class@7.3-23 r-cluster@2.1.8.1 r-compositions@2.0-9 r-delayedmatrixstats@1.32.0 r-diptest@0.77-2 r-edger@4.8.0 r-fpc@2.2-13 r-gplots@3.2.0 r-hexbin@1.28.5 r-limma@3.66.0 r-matrixgenerics@1.22.0 r-matrixstats@1.5.0 r-mixtools@2.0.0.1 r-rarpack@0.11-0 r-rcolorbrewer@1.1-3 r-rhdf5@2.54.0 r-ruvseq@1.44.0 r-singlecellexperiment@1.32.0 r-sparsearray@1.10.2 r-sparsematrixstats@1.22.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/scone
Licenses: Artistic License 2.0
Build system: r
Synopsis: Single cell overview of normalized expression data
Description:

SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.

r-asgsca 1.44.0
Propagated dependencies: r-mass@7.3-65 r-matrix@1.7-4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ASGSCA
Licenses: GPL 3
Build system: r
Synopsis: Analysis of associations between multiple genotypes and traits
Description:

The package ASGSCA (Association Study using Generalized Structured Component Analysis) provides tools to model and test the association between multiple genotypes and multiple traits, taking into account the prior biological knowledge. Genes, and clinical pathways are incorporated in the model as latent variables.

r-coregx 2.14.0
Propagated dependencies: r-bench@1.1.4 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-bumpymatrix@1.18.0 r-checkmate@2.3.3 r-crayon@1.5.3 r-data-table@1.17.8 r-glue@1.8.0 r-lsa@0.73.3 r-matrixgenerics@1.22.0 r-multiassayexperiment@1.36.1 r-piano@2.26.0 r-rlang@1.1.6 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/CoreGx
Licenses: GPL 3+
Build system: r
Synopsis: Classes and functions to serve as the basis for other Gx packages
Description:

This package provides a collection of functions and classes which serve as the foundation for packages such as PharmacoGx and RadioGx. It was created to abstract shared functionality to increase ease of maintainability and reduce code repetition in current and future Gx suite programs. Major features include a CoreSet class, from which RadioSet and PharmacoSet are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating AUC or SF are included.

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-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-gypsum 1.6.0
Propagated dependencies: r-filelock@1.0.3 r-httr2@1.2.1 r-jsonlite@2.0.0 r-rappdirs@0.3.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ArtifactDB/gypsum-R
Licenses: Expat
Build system: r
Synopsis: Interface to the gypsum REST API
Description:

This package provides a client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various administrative and management tasks. Check out the documentation at https://github.com/ArtifactDB/gypsum-worker for more details.

r-hgu95a-db 3.13.0
Propagated dependencies: r-annotationdbi@1.72.0 r-org-hs-eg-db@3.22.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/hgu95a.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix HG_U95A Array annotation data (chip hgu95a)
Description:

This package provides Affymetrix HG_U95A Array annotation data (chip hgu95a) assembled using data from public repositories.

r-arrayqualitymetrics 3.64.0
Propagated dependencies: r-affy@1.88.0 r-affyplm@1.86.0 r-beadarray@2.58.0 r-biobase@2.70.0 r-genefilter@1.92.0 r-gridsvg@1.7-7 r-hmisc@5.2-4 r-hwriter@1.3.2.1 r-lattice@0.22-7 r-latticeextra@0.6-31 r-limma@3.66.0 r-rcolorbrewer@1.1-3 r-setrng@2024.2-1 r-svglite@2.2.2 r-vsn@3.78.0 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/arrayQualityMetrics
Licenses: LGPL 2.0+
Build system: r
Synopsis: Quality metrics report for microarray data sets
Description:

This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.

r-deconstructsigs 1.8.0
Propagated dependencies: r-bsgenome@1.78.0 r-bsgenome-hsapiens-ucsc-hg19@1.4.3 r-genomeinfodb@1.46.0 r-reshape2@1.4.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/raerose01/deconstructSigs
Licenses: GPL 2+
Build system: r
Synopsis: Identifies signatures present in a tumor sample
Description:

This package takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile.

r-densvis 1.20.1
Propagated dependencies: r-assertthat@0.2.1 r-basilisk@1.22.0 r-irlba@2.3.5.1 r-rcpp@1.1.0 r-reticulate@1.44.1 r-rtsne@0.17
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/densvis
Licenses: Expat
Build system: r
Synopsis: Density-preserving data visualization via non-linear dimensionality reduction
Description:

This package implements the density-preserving modification to t-SNE and UMAP described by Narayan et al. (2020) <doi:10.1101/2020.05.12.077776>. den-SNE and densMAP aim to enable more accurate visual interpretation of high-dimensional datasets by producing lower-dimensional embeddings that accurately represent the heterogeneity of the original high-dimensional space, enabling the identification of homogeneous and heterogeneous cell states. This accuracy is accomplished by including in the optimisation process a term which considers the local density of points in the original high-dimensional space. This can help to create visualisations that are more representative of heterogeneity in the original high-dimensional space.

r-interactionset 1.38.0
Propagated dependencies: r-biocgenerics@0.56.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-matrix@1.7-4 r-rcpp@1.1.0 r-s4vectors@0.48.0 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/InteractionSet
Licenses: GPL 3
Build system: r
Synopsis: Base classes for storing genomic interaction data
Description:

This package provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.

r-absseq 1.64.0
Propagated dependencies: r-limma@3.66.0 r-locfit@1.5-9.12
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ABSSeq
Licenses: GPL 3+
Build system: r
Synopsis: RNA-Seq analysis based on modelling absolute expression differences
Description:

This package implements a new RNA-Seq analysis method and integrates two modules: a basic model for pairwise comparison and a linear model for complex design. RNA-Seq quantifies gene expression with reads count, which usually consists of conditions (or treatments) and several replicates for each condition. This software infers differential expression directly by the counts difference between conditions. It assumes that the sum counts difference between conditions follow a negative binomial distribution. In addition, ABSSeq moderates the fold-changes by two steps: the expression level and gene-specific dispersion, that might facilitate the gene ranking by fold-change and visualization.

r-scry 1.22.0
Propagated dependencies: r-biocsingular@1.26.1 r-delayedarray@0.36.0 r-glmpca@0.2.0 r-matrix@1.7-4 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/scry.html
Licenses: Artistic License 2.0
Build system: r
Synopsis: Small-count analysis methods for high-dimensional data
Description:

Many modern biological datasets consist of small counts that are not well fit by standard linear-Gaussian methods such as principal component analysis. This package provides implementations of count-based feature selection and dimension reduction algorithms. These methods can be used to facilitate unsupervised analysis of any high-dimensional data such as single-cell RNA-seq.

r-pd-mapping50k-hind240 3.12.0
Propagated dependencies: r-biostrings@2.78.0 r-dbi@1.2.3 r-iranges@2.44.0 r-oligo@1.74.0 r-oligoclasses@1.72.0 r-rsqlite@2.4.4 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/pd.mapping50k.hind240
Licenses: Artistic License 2.0
Build system: r
Synopsis: Platform Design Info for Affymetrix Mapping50K_Hind240
Description:

This package provides platform design info for Affymetrix Mapping50K_Hind240.

r-geoquery 2.78.0
Propagated dependencies: r-biobase@2.70.0 r-curl@7.0.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-httr2@1.2.1 r-limma@3.66.0 r-magrittr@2.0.4 r-r-utils@2.13.0 r-readr@2.1.6 r-rentrez@1.2.4 r-rvest@1.0.5 r-s4vectors@0.48.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-tidyr@1.3.1 r-xml2@1.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/seandavi/GEOquery/
Licenses: GPL 2
Build system: r
Synopsis: Get data from NCBI Gene Expression Omnibus (GEO)
Description:

The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.

r-mus-musculus 1.3.1
Propagated dependencies: r-annotationdbi@1.72.0 r-genomicfeatures@1.62.0 r-go-db@3.22.0 r-org-mm-eg-db@3.22.0 r-organismdbi@1.52.0 r-txdb-mmusculus-ucsc-mm10-knowngene@3.10.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Mus.musculus
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for the Mus.musculus object
Description:

This package contains the Mus.musculus object to access data from several related annotation packages.

r-affycontam 1.68.0
Propagated dependencies: r-affy@1.88.0 r-affydata@1.58.0 r-biobase@2.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/affyContam/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Structured corruption of Affymetrix CEL file data
Description:

Microarray quality assessment is a major concern of microarray analysts. This package provides some simple approaches to in silico creation of quality problems in CEL-level data to help evaluate performance of quality metrics.

r-multiassayexperiment 1.36.1
Propagated dependencies: r-biobase@2.70.0 r-biocbaseutils@1.12.0 r-biocgenerics@0.56.0 r-delayedarray@0.36.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-matrixgenerics@1.22.0 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://waldronlab.io/MultiAssayExperiment/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Integration of multi-omics experiments in Bioconductor
Description:

MultiAssayExperiment harmonizes data management of multiple assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames.

r-consensusclusterplus 1.74.0
Propagated dependencies: r-all@1.52.0 r-biobase@2.70.0 r-cluster@2.1.8.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ConsensusClusterPlus
Licenses: GPL 2
Build system: r
Synopsis: Clustering algorithm
Description:

This package provides an implementation of an algorithm for determining cluster count and membership by stability evidence in unsupervised analysis.

r-ensdb-hsapiens-v86 2.99.0
Propagated dependencies: r-ensembldb@2.34.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/EnsDb.Hsapiens.v86
Licenses: Artistic License 2.0
Build system: r
Synopsis: Ensembl based annotation package
Description:

This package exposes an annotation database generated from Ensembl.

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Total results: 68658