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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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r-multiassayexperiment 1.34.0
Propagated dependencies: r-biobase@2.68.0 r-biocbaseutils@1.10.0 r-biocgenerics@0.54.0 r-delayedarray@0.34.1 r-genomicranges@1.60.0 r-iranges@2.42.0 r-s4vectors@0.46.0 r-summarizedexperiment@1.38.1 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
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-arraymvout 1.66.0
Propagated dependencies: r-affy@1.86.0 r-affycontam@1.66.0 r-biobase@2.68.0 r-lumi@2.60.0 r-mdqc@1.70.0 r-parody@1.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/arrayMvout
Licenses: Artistic License 2.0
Synopsis: Multivariate outlier detection for expression array QA
Description:

This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate.

r-hsmmsinglecell 1.28.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/HSMMSingleCell/
Licenses: Artistic License 2.0
Synopsis: Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)
Description:

Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell.

r-ggpicrust2 2.1.2
Propagated dependencies: r-aplot@0.2.5 r-dplyr@1.1.4 r-ggh4x@0.3.1 r-ggplot2@3.5.2 r-ggplotify@0.1.2 r-ggprism@1.0.6 r-ggraph@2.2.1 r-magrittr@2.0.3 r-patchwork@1.3.0 r-progress@1.2.3 r-readr@2.1.5 r-tibble@3.2.1 r-tidygraph@1.3.1 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/cafferychen777/ggpicrust2
Licenses: Expat
Synopsis: Make PICRUSt2 output analysis and visualization easier
Description:

This package provides a convenient way to analyze and visualize PICRUSt2 output with pre-defined plots and functions. It allows for generating statistical plots about microbiome functional predictions and offers customization options. It features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. It streamlines the PICRUSt2 analysis and visualization process.

r-metagenomeseq 1.50.0
Propagated dependencies: r-biobase@2.68.0 r-foreach@1.5.2 r-glmnet@4.1-8 r-gplots@3.2.0 r-limma@3.64.1 r-matrix@1.7-3 r-matrixstats@1.5.0 r-rcolorbrewer@1.1-3 r-wrench@1.26.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/HCBravoLab/metagenomeSeq
Licenses: Artistic License 2.0
Synopsis: Statistical analysis for sparse high-throughput sequencing
Description:

MetagenomeSeq is designed to determine features (be it OTU, species, etc.) that are differentially abundant between two or more groups of multiple samples. This package is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.

r-organismdbi 1.50.0
Propagated dependencies: r-annotationdbi@1.70.0 r-biobase@2.68.0 r-biocgenerics@0.54.0 r-biocmanager@1.30.25 r-dbi@1.2.3 r-genomicfeatures@1.60.0 r-genomicranges@1.60.0 r-graph@1.86.0 r-iranges@2.42.0 r-rbgl@1.84.0 r-s4vectors@0.46.0 r-txdbmaker@1.4.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/OrganismDbi
Licenses: Artistic License 2.0
Synopsis: Software to enable the smooth interfacing of database packages
Description:

The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.

r-do-db 2.9
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/DO.db/
Licenses: Artistic License 2.0
Synopsis: Annotation maps describing the entire Disease Ontology
Description:

This package provides a set of annotation maps describing the entire Disease Ontology.

r-chipexoqual 1.32.0
Propagated dependencies: r-biocparallel@1.42.0 r-biovizbase@1.56.0 r-broom@1.0.8 r-data-table@1.17.4 r-dplyr@1.1.4 r-genomeinfodb@1.44.0 r-genomicalignments@1.44.0 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-hexbin@1.28.5 r-iranges@2.42.0 r-rcolorbrewer@1.1-3 r-rmarkdown@2.29 r-rsamtools@2.24.0 r-s4vectors@0.46.0 r-scales@1.4.0 r-viridis@0.6.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/keleslab/ChIPexoQual
Licenses: GPL 2+
Synopsis: Quality control pipeline for ChIP-exo/nexus data
Description:

This package provides a quality control pipeline for ChIP-exo/nexus sequencing data.

r-ciara 0.1.0
Propagated dependencies: r-biobase@2.68.0 r-ggplot2@3.5.2 r-ggraph@2.2.1 r-magrittr@2.0.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/package=CIARA
Licenses: Artistic License 2.0
Synopsis: Cluster-independent algorithm for rare cell types identification
Description:

This is a package to support identification of markers of rare cell types by looking at genes whose expression is confined in small regions of the expression space.

r-aneufinder 1.35.0
Propagated dependencies: r-aneufinderdata@1.36.0 r-bamsignals@1.40.0 r-biocgenerics@0.54.0 r-biostrings@2.76.0 r-cowplot@1.1.3 r-dnacopy@1.82.0 r-doparallel@1.0.17 r-ecp@3.1.6 r-foreach@1.5.2 r-genomeinfodb@1.44.0 r-genomicalignments@1.44.0 r-genomicranges@1.60.0 r-ggdendro@0.2.0 r-ggplot2@3.5.2 r-ggrepel@0.9.6 r-iranges@2.42.0 r-mclust@6.1.1 r-reshape2@1.4.4 r-rsamtools@2.24.0 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AneuFinder/
Licenses: Artistic License 2.0
Synopsis: Copy number variation analysis in single-cell-sequencing data
Description:

This package implements functions for copy number variant calling, plotting, export and analysis from whole-genome single cell sequencing data.

r-ensdb-mmusculus-v79 2.99.0
Propagated dependencies: r-ensembldb@2.32.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/EnsDb.Mmusculus.v79
Licenses: Artistic License 2.0
Synopsis: Ensembl based annotation package
Description:

This package exposes an annotation database generated from Ensembl.

r-roar 1.44.1
Propagated dependencies: r-biocgenerics@0.54.0 r-genomeinfodb@1.44.0 r-genomicalignments@1.44.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-rtracklayer@1.68.0 r-s4vectors@0.46.0 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/vodkatad/roar/
Licenses: GPL 3
Synopsis: Identify differential APA usage from RNA-seq alignments
Description:

This package provides tools for identifying preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.

r-manor 1.80.0
Propagated dependencies: r-glad@2.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://bioinfo.curie.fr/projects/manor/index.html
Licenses: GPL 2
Synopsis: CGH micro-array normalization
Description:

This package ofers functions for importation, normalization, visualization, and quality control to correct identified sources of variability in array of CGH experiments.

r-org-eck12-eg-db 3.21.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/org.EcK12.eg.db
Licenses: Artistic License 2.0
Synopsis: Genome wide annotation for E coli strain K12
Description:

This package provides genome wide annotation for E coli strain K12, primarily based on mapping using Entrez Gene identifiers. Entrez Gene is National Center for Biotechnology Information (NCBI)’s database for gene-specific information. Entrez Gene maintains records from genomes which have been completely sequenced, which have an active research community to submit gene-specific information, or which are scheduled for intense sequence analysis.

r-ldheatmap 1.0-6
Propagated dependencies: r-genetics@1.3.8.1.3 r-rcpp@1.0.14 r-snpstats@1.58.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://stat.sfu.ca/statgen/research/ldheatmap.html
Licenses: GPL 3
Synopsis: Graphical display of pairwise linkage disequilibria between SNPs
Description:

This package provides tools to produce a graphical display, as a heat map, of measures of pairwise linkage disequilibria between SNPs. Users may optionally include the physical locations or genetic map distances of each SNP on the plot.

r-enrichplot 1.28.2
Propagated dependencies: r-aplot@0.2.5 r-dose@4.2.0 r-ggfun@0.1.8 r-ggnewscale@0.5.1 r-ggplot2@3.5.2 r-ggrepel@0.9.6 r-ggtangle@0.0.6 r-ggtree@3.16.0 r-gosemsim@2.34.0 r-igraph@2.1.4 r-magrittr@2.0.3 r-plyr@1.8.9 r-purrr@1.0.4 r-rcolorbrewer@1.1-3 r-reshape2@1.4.4 r-rlang@1.1.6 r-scatterpie@0.2.4 r-yulab-utils@0.2.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/GuangchuangYu/enrichplot
Licenses: Artistic License 2.0
Synopsis: Visualization of functional enrichment result
Description:

The enrichplot package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analyses. All the visualization methods are developed based on ggplot2 graphics.

r-guitar 2.24.0
Propagated dependencies: r-annotationdbi@1.70.0 r-dplyr@1.1.4 r-genomicfeatures@1.60.0 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-knitr@1.50 r-magrittr@2.0.3 r-rtracklayer@1.68.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Guitar
Licenses: GPL 2
Synopsis: Visualize genomic features
Description:

This package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.

r-globaltest 5.62.0
Propagated dependencies: r-annotate@1.86.0 r-annotationdbi@1.70.0 r-biobase@2.68.0 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/globaltest
Licenses: GPL 2+
Synopsis: Test groups of covariates for association with a response variable
Description:

The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.

r-gofuncr 1.28.0
Propagated dependencies: r-annotationdbi@1.70.0 r-genomicranges@1.60.0 r-gtools@3.9.5 r-iranges@2.42.0 r-mapplots@1.5.2 r-rcpp@1.0.14 r-vioplot@0.5.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GOfuncR/
Licenses: GPL 2+
Synopsis: Gene ontology enrichment using FUNC
Description:

GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages (Homo.sapiens by default); the GO-graph is included in the package and updated regularly. GOfuncR provides the standard candidate vs background enrichment analysis using the hypergeometric test, as well as three additional tests:

  1. the Wilcoxon rank-sum test that is used when genes are ranked,

  2. a binomial test that is used when genes are associated with two counts, and

  3. a Chi-square or Fisher's exact test that is used in cases when genes are associated with four counts.

To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.

r-variantannotation 1.54.1
Propagated dependencies: r-annotationdbi@1.70.0 r-biobase@2.68.0 r-biocgenerics@0.54.0 r-biostrings@2.76.0 r-bsgenome@1.76.0 r-dbi@1.2.3 r-genomeinfodb@1.44.0 r-genomicfeatures@1.60.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-matrixgenerics@1.20.0 r-rhtslib@3.4.0 r-rsamtools@2.24.0 r-rtracklayer@1.68.0 r-s4vectors@0.46.0 r-summarizedexperiment@1.38.1 r-xvector@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/VariantAnnotation
Licenses: Artistic License 2.0
Synopsis: Package for annotation of genetic variants
Description:

This R package can annotate variants, compute amino acid coding changes and predict coding outcomes.

r-flowclust 3.46.0
Dependencies: gsl@2.8
Propagated dependencies: r-biobase@2.68.0 r-biocgenerics@0.54.0 r-flowcore@2.20.0 r-graph@1.86.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/flowClust
Licenses: Artistic License 2.0
Synopsis: Clustering for flow cytometry
Description:

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

r-fishpond 2.14.0
Propagated dependencies: r-abind@1.4-8 r-genomicranges@1.60.0 r-gtools@3.9.5 r-iranges@2.42.0 r-jsonlite@2.0.0 r-matrix@1.7-3 r-matrixstats@1.5.0 r-qvalue@2.40.0 r-s4vectors@0.46.0 r-singlecellexperiment@1.30.1 r-summarizedexperiment@1.38.1 r-svmisc@1.4.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/mikelove/fishpond
Licenses: GPL 2
Synopsis: Downstream methods and tools for expression data
Description:

The fishpond package contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains a number of utilities for working with Salmon and Alevin quantification files.

r-pfam-db 3.21.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/PFAM.db
Licenses: Artistic License 2.0
Synopsis: Set of protein ID mappings for PFAM
Description:

This package provides a set of protein ID mappings for PFAM, assembled using data from public repositories.

r-seqarray 1.48.0
Propagated dependencies: r-biostrings@2.76.0 r-digest@0.6.37 r-gdsfmt@1.44.0 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/zhengxwen/SeqArray
Licenses: GPL 3
Synopsis: Data management of large-scale whole-genome sequence variant calls
Description:

This package supports data management of large-scale whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray GDS files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.

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Total results: 45109