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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-bisquerna 1.0.5
Propagated dependencies: r-biobase@2.70.0 r-limsolve@2.0.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.biorxiv.org/content/10.1101/669911v1
Licenses: GPL 3
Build system: r
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-txdb-dmelanogaster-ucsc-dm6-ensgene 3.12.0
Propagated dependencies: r-annotationdbi@1.72.0 r-genomicfeatures@1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/TxDb.Dmelanogaster.UCSC.dm6.ensGene
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for TxDb object(s)
Description:

This package exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

r-genie3 1.32.0
Propagated dependencies: r-dplyr@1.1.4 r-reshape2@1.4.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GENIE3
Licenses: GPL 2+
Build system: r
Synopsis: Gene network inference with ensemble of trees
Description:

This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.

r-bodymaprat 1.26.0
Propagated dependencies: r-experimenthub@3.0.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/bodymapRat
Licenses: CC-BY 4.0
Build system: r
Synopsis: Experimental dataset from the rat BodyMap project
Description:

This package contains a SummarizedExperiment from the Yu et al. (2013) paper that performed the rat BodyMap across 11 organs and 4 developmental stages. Raw FASTQ files were downloaded and mapped using STAR. Data is available on ExperimentHub as a data package.

r-wavcluster 2.44.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-foreach@1.5.2 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-hmisc@5.2-4 r-iranges@2.44.0 r-mclust@6.1.2 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinr@4.2-36 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/wavClusteR/
Licenses: GPL 2
Build system: r
Synopsis: Identification of RNA-protein interaction sites in PAR-CLIP data
Description:

This package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non-experimental sources by a non- parametric mixture model. The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post-processing of the results, data export for UCSC genome browser visualization and motif search analysis are provided. In addition, the package integrates RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. While wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).

r-genomicscores 2.22.0
Propagated dependencies: r-annotationhub@4.0.0 r-biobase@2.70.0 r-biocfilecache@3.0.0 r-biocgenerics@0.56.0 r-biocmanager@1.30.27 r-biostrings@2.78.0 r-delayedarray@0.36.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-hdf5array@1.38.0 r-httr@1.4.7 r-iranges@2.44.0 r-rhdf5@2.54.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/rcastelo/GenomicScores/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Work with genome-wide position-specific scores
Description:

This package provides infrastructure to store and access genome-wide position-specific scores within R and Bioconductor.

r-biocdockermanager 1.11.0
Propagated dependencies: docker@20.10.27 r-dplyr@1.1.4 r-httr@1.4.7 r-memoise@2.0.1 r-readr@2.1.6 r-whisker@0.4.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BiocDockerManager
Licenses: Artistic License 2.0
Build system: r
Synopsis: Access and manage Bioconductor Docker images
Description:

This package works analogous to BiocManager but for Docker images. Use the BiocDockerManager package to install and manage Docker images provided by the Bioconductor project.

r-gsvadata 1.46.0
Propagated dependencies: r-biobase@2.70.0 r-gseabase@1.72.0 r-hgu95a-db@3.13.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GSVAdata
Licenses: Artistic License 2.0
Build system: r
Synopsis: Data employed in the vignette of the GSVA package
Description:

This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010; Costa et al. FEBS J, 288:2311-2331, 2021.

r-roar 1.46.0
Propagated dependencies: r-biocgenerics@0.56.0 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/vodkatad/roar/
Licenses: GPL 3
Build system: r
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-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-qfeatures 1.20.0
Propagated dependencies: r-annotationfilter@1.34.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-igraph@2.2.1 r-iranges@2.44.0 r-lazyeval@0.2.2 r-mscoreutils@1.21.0 r-multiassayexperiment@1.36.1 r-plotly@4.11.0 r-protgenerics@1.42.0 r-reshape2@1.4.5 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0 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
Build system: r
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-awst 1.18.0
Propagated dependencies: r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/drisso/awst
Licenses: Expat
Build system: r
Synopsis: Asymmetric within-sample transformation
Description:

This package awst (Asymmetric Within-Sample Transformation) that regularizes RNA-seq read counts and reduces the effect of noise on the classification of samples. AWST comprises two main steps: standardization and smoothing. These steps transform gene expression data to reduce the noise of the lowly expressed features, which suffer from background effects and low signal-to-noise ratio, and the influence of the highly expressed features, which may be the result of amplification bias and other experimental artifacts.

r-yapsa 1.36.0
Propagated dependencies: r-biostrings@2.78.0 r-bsgenome-hsapiens-ucsc-hg19@1.4.3 r-circlize@0.4.16 r-complexheatmap@2.26.0 r-corrplot@0.95 r-dendextend@1.19.1 r-doparallel@1.0.17 r-dplyr@1.1.4 r-genomicranges@1.62.0 r-getoptlong@1.0.5 r-ggbeeswarm@0.7.2 r-ggplot2@4.0.1 r-gridextra@2.3 r-gtrellis@1.42.0 r-keggrest@1.50.0 r-limsolve@2.0.1 r-magrittr@2.0.4 r-pmcmrplus@1.9.12 r-pracma@2.4.6 r-reshape2@1.4.5 r-seqinfo@1.0.0 r-somaticsignatures@2.46.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/YAPSA/
Licenses: GPL 3
Build system: r
Synopsis: Yet another package for signature analysis
Description:

This package provides functions and routines useful in the analysis of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, functions to perform a signature analysis with known signatures and a signature analysis on stratified mutational catalogue (SMC) are provided.

r-scdd 1.34.0
Propagated dependencies: r-arm@1.14-4 r-biocparallel@1.44.0 r-ebseq@2.8.0 r-fields@17.1 r-ggplot2@4.0.1 r-mclust@6.1.2 r-outliers@0.15 r-s4vectors@0.48.0 r-scran@1.38.0 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/kdkorthauer/scDD
Licenses: GPL 2
Build system: r
Synopsis: Mixture modeling of single-cell RNA-seq data
Description:

This package implements a method to analyze single-cell RNA-seq data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.

r-clusterexperiment 2.30.0
Propagated dependencies: r-ape@5.8-1 r-biocgenerics@0.56.0 r-biocsingular@1.26.1 r-cluster@2.1.8.1 r-delayedarray@0.36.0 r-edger@4.8.0 r-hdf5array@1.38.0 r-kernlab@0.9-33 r-limma@3.66.0 r-locfdr@1.1-8 r-matrix@1.7-4 r-matrixstats@1.5.0 r-mbkmeans@1.26.0 r-nmf@0.28 r-phylobase@0.8.12 r-pracma@2.4.6 r-rcolorbrewer@1.1-3 r-rcpp@1.1.0 r-s4vectors@0.48.0 r-scales@1.4.0 r-singlecellexperiment@1.32.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-zinbwave@1.32.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/clusterExperiment/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Compare clusterings for single-cell sequencing
Description:

This package provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA expression data sets.

r-beaddatapackr 1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BeadDataPackR
Licenses: GPL 2
Build system: r
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-convert 1.86.0
Propagated dependencies: r-biobase@2.70.0 r-limma@3.66.0 r-marray@1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://bioinf.wehi.edu.au/limma/convert.html
Licenses: LGPL 2.0+
Build system: r
Synopsis: Convert microarray data objects
Description:

This package defines coerce methods for microarray data objects.

r-sictools 1.40.0
Dependencies: ncurses@6.2.20210619
Propagated dependencies: r-biostrings@2.78.0 r-doparallel@1.0.17 r-genomicranges@1.62.0 r-iranges@2.44.0 r-matrixstats@1.5.0 r-plyr@1.8.9 r-rsamtools@2.26.0 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/SICtools
Licenses: GPL 2+
Build system: r
Synopsis: Find SNV/Indel differences between two bam files with near relationship
Description:

This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison through each base position across the genome region of interest. The difference is inferred by Fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.

r-s4vectors 0.48.0
Propagated dependencies: r-biocgenerics@0.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/S4Vectors
Licenses: Artistic License 2.0
Build system: r
Synopsis: S4 implementation of vectors and lists
Description:

The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself.

r-org-ce-eg-db 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/org.Ce.eg.db/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Genome wide annotation for Worm
Description:

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model worm Caenorhabditis elegans.

r-asics 2.26.0
Propagated dependencies: r-biocparallel@1.44.0 r-ggplot2@4.0.1 r-glmnet@4.1-10 r-gridextra@2.3 r-matrix@1.7-4 r-mvtnorm@1.3-3 r-pepsnmr@1.28.0 r-plyr@1.8.9 r-quadprog@1.5-8 r-ropls@1.42.0 r-summarizedexperiment@1.40.0 r-zoo@1.8-14
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ASICS
Licenses: GPL 2+
Build system: r
Synopsis: Automatic statistical identification in complex spectra
Description:

ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty.

r-interactivedisplay 1.48.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biocgenerics@0.56.0 r-biocmanager@1.30.27 r-category@2.76.0 r-ggplot2@4.0.1 r-gridsvg@1.7-7 r-interactivedisplaybase@1.48.0 r-plyr@1.8.9 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-shiny@1.11.1 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/interactiveDisplay
Licenses: Artistic License 2.0
Build system: r
Synopsis: Package for Shiny web displays of Bioconductor objects
Description:

This package offers interactive Shiny displays for Bioconductor objects. In addition, this package empowers users to develop engaging visualizations and interfaces for working with Bioconductor data.

r-ebarrays 2.74.0
Propagated dependencies: r-biobase@2.70.0 r-cluster@2.1.8.1 r-lattice@0.22-7
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/EBarrays/
Licenses: GPL 2+
Build system: r
Synopsis: Gene clustering and differential expression identification
Description:

EBarrays provides tools for the analysis of replicated/unreplicated microarray data.

r-minet 3.68.0
Propagated dependencies: r-infotheo@1.2.0.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://minet.meyerp.com
Licenses: Artistic License 2.0
Build system: r
Synopsis: Mutual information networks
Description:

This package implements various algorithms for inferring mutual information networks from data.

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Total results: 69112