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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-biocneighbors 2.2.0
Propagated dependencies: r-assorthead@1.2.0 r-rcpp@1.0.14
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BiocNeighbors
Licenses: GPL 3
Synopsis: Nearest Neighbor Detection for Bioconductor packages
Description:

This package implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. The exact algorithm is implemented using pre-clustering with the k-means algorithm. Functions are also provided to search for all neighbors within a given distance. Parallelization is achieved for all methods using the BiocParallel framework.

r-bioccheck 1.44.2
Propagated dependencies: r-biocbaseutils@1.10.0 r-biocfilecache@2.16.0 r-biocmanager@1.30.25 r-biocviews@1.76.0 r-callr@3.7.6 r-cli@3.6.5 r-codetools@0.2-20 r-graph@1.86.0 r-httr2@1.1.2 r-knitr@1.50 r-rvest@1.0.5 r-stringdist@0.9.15
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BiocCheck
Licenses: Artistic License 2.0
Synopsis: Executes Bioconductor-specific package checks
Description:

This package contains tools to perform additional quality checks on R packages that are to be submitted to the Bioconductor repository.

r-derfinderhelper 1.42.0
Propagated dependencies: r-iranges@2.42.0 r-matrix@1.7-3 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/leekgroup/derfinderHelper
Licenses: Artistic License 2.0
Synopsis: Helper for derfinder
Description:

This package speeds up the derfinder package when using multiple cores. It is particularly useful when using BiocParallel and it helps reduce the time spent loading the full derfinder package when running the F-statistics calculation in parallel.

r-epidish 2.24.0
Propagated dependencies: r-e1071@1.7-16 r-locfdr@1.1-8 r-mass@7.3-65 r-matrix@1.7-3 r-matrixstats@1.5.0 r-quadprog@1.5-8 r-stringr@1.5.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/sjczheng/EpiDISH
Licenses: GPL 2
Synopsis: Epigenetic dissection of intra-sample-heterogeneity
Description:

EpiDISH is a R package to infer the proportions of a priori known cell-types present in a sample representing a mixture of such cell-types. Right now, the package can be used on DNAm data of whole blood, generic epithelial tissue and breast tissue. Besides, the package provides a function that allows the identification of differentially methylated cell-types and their directionality of change in Epigenome-Wide Association Studies.

r-piano 2.24.0
Propagated dependencies: r-biobase@2.68.0 r-biocgenerics@0.54.0 r-dt@0.33 r-fgsea@1.34.0 r-gplots@3.2.0 r-htmlwidgets@1.6.4 r-igraph@2.1.4 r-marray@1.86.0 r-relations@0.6-15 r-scales@1.4.0 r-shiny@1.10.0 r-shinydashboard@0.7.3 r-shinyjs@2.1.0 r-visnetwork@2.1.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://varemo.github.io/piano/
Licenses: GPL 2+
Synopsis: Platform for integrative analysis of omics data
Description:

Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. The package contains functions for combining the results of multiple runs of gene set analyses.

r-mfuzz 2.68.0
Propagated dependencies: r-biobase@2.68.0 r-e1071@1.7-16 r-tkwidgets@1.86.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://mfuzz.sysbiolab.eu/
Licenses: GPL 2
Synopsis: Soft clustering of time series gene expression data
Description:

This is a package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface).

r-bayesspace 1.17.0
Propagated dependencies: r-arrow@21.0.0 r-assertthat@0.2.1 r-biocfilecache@2.16.0 r-biocparallel@1.42.0 r-biocsingular@1.24.0 r-coda@0.19-4.1 r-dirichletreg@0.7-1 r-dplyr@1.1.4 r-ggplot2@3.5.2 r-magrittr@2.0.3 r-matrix@1.7-3 r-mclust@6.1.1 r-microbenchmark@1.5.0 r-purrr@1.0.4 r-rcpp@1.0.14 r-rcpparmadillo@14.4.3-1 r-rcppdist@0.1.1 r-rcppprogress@0.4.2 r-rcurl@1.98-1.17 r-rhdf5@2.52.0 r-rjson@0.2.23 r-rlang@1.1.6 r-s4vectors@0.46.0 r-scales@1.4.0 r-scater@1.36.0 r-scran@1.36.0 r-singlecellexperiment@1.30.1 r-summarizedexperiment@1.38.1 r-tibble@3.2.1 r-tidyr@1.3.1 r-xgboost@1.7.11.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.ezstatconsulting.com/BayesSpace/
Licenses: Expat
Synopsis: Clustering and resolution enhancement of spatial transcriptomes
Description:

This package provides tools for clustering and enhancing the resolution of spatial gene expression experiments. BayesSpace clusters a low-dimensional representation of the gene expression matrix, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.

r-xbseq 1.22.0
Propagated dependencies: r-biobase@2.68.0 r-deseq2@1.48.1 r-dplyr@1.1.4 r-ggplot2@3.5.2 r-locfit@1.5-9.12 r-magrittr@2.0.3 r-matrixstats@1.5.0 r-pracma@2.4.4 r-roar@1.44.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/Liuy12/XBSeq
Licenses: GPL 3+
Synopsis: Test for differential expression for RNA-seq data
Description:

XBSeq is a novel algorithm for testing RNA-seq differential expression (DE), where a statistical model was established based on the assumption that observed signals are the convolution of true expression signals and sequencing noises. The mapped reads in non-exonic regions are considered as sequencing noises, which follows a Poisson distribution. Given measurable observed signal and background noise from RNA-seq data, true expression signals, assuming governed by the negative binomial distribution, can be delineated and thus the accurate detection of differential expressed genes.

r-biocstyle 2.36.0
Propagated dependencies: r-biocmanager@1.30.25 r-bookdown@0.43 r-knitr@1.50 r-rmarkdown@2.29 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BiocStyle
Licenses: Artistic License 2.0
Synopsis: Bioconductor formatting styles
Description:

This package provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.

r-methylumi 2.54.0
Propagated dependencies: r-annotate@1.86.0 r-annotationdbi@1.70.0 r-biobase@2.68.0 r-biocgenerics@0.54.0 r-fdb-infiniummethylation-hg19@2.2.0 r-genefilter@1.90.0 r-genomeinfodb@1.44.0 r-genomicfeatures@1.60.0 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-illuminaio@0.50.0 r-iranges@2.42.0 r-lattice@0.22-7 r-matrixstats@1.5.0 r-minfi@1.54.1 r-reshape2@1.4.4 r-s4vectors@0.46.0 r-scales@1.4.0 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/methylumi
Licenses: GPL 2
Synopsis: Handle Illumina methylation data
Description:

This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

r-txdbmaker 1.4.1
Propagated dependencies: r-annotationdbi@1.70.0 r-biobase@2.68.0 r-biocgenerics@0.54.0 r-biocio@1.18.0 r-biomart@2.64.0 r-dbi@1.2.3 r-genomeinfodb@1.44.0 r-genomicfeatures@1.60.0 r-genomicranges@1.60.0 r-httr@1.4.7 r-iranges@2.42.0 r-rjson@0.2.23 r-rsqlite@2.3.11 r-rtracklayer@1.68.0 r-s4vectors@0.46.0 r-ucsc-utils@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/txdbmaker
Licenses: Artistic License 2.0
Synopsis: Tools for making TxDb objects from genomic annotations
Description:

This package provides a set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.

r-marray 1.86.0
Propagated dependencies: r-limma@3.64.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/marray
Licenses: LGPL 2.0+
Synopsis: Exploratory analysis for two-color spotted microarray data
Description:

This package contains class definitions for two-color spotted microarray data. It also includes functions for data input, diagnostic plots, normalization and quality checking.

r-ballgown 2.40.0
Propagated dependencies: r-biobase@2.68.0 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-limma@3.64.1 r-rcolorbrewer@1.1-3 r-rtracklayer@1.68.0 r-s4vectors@0.46.0 r-sva@3.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ballgown
Licenses: Artistic License 2.0
Synopsis: Flexible, isoform-level differential expression analysis
Description:

This package provides tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.

r-glimma 2.18.0
Propagated dependencies: r-deseq2@1.48.1 r-edger@4.6.2 r-htmlwidgets@1.6.4 r-jsonlite@2.0.0 r-limma@3.64.1 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/Shians/Glimma
Licenses: LGPL 3
Synopsis: Interactive HTML graphics
Description:

This package generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.

r-chipseq 1.58.0
Propagated dependencies: r-biocgenerics@0.54.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-lattice@0.22-7 r-s4vectors@0.46.0 r-shortread@1.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/chipseq
Licenses: Artistic License 2.0
Synopsis: Package for analyzing ChIPseq data
Description:

This package provides tools for processing short read data from ChIPseq experiments.

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-escape 2.4.0
Propagated dependencies: r-aucell@1.30.1 r-biocparallel@1.42.0 r-dplyr@1.1.4 r-ggdist@3.3.3 r-ggplot2@3.5.2 r-ggpointdensity@0.2.0 r-ggridges@0.5.6 r-gseabase@1.70.0 r-gsva@2.2.0 r-matrix@1.7-3 r-matrixgenerics@1.20.0 r-msigdb@1.16.0 r-patchwork@1.3.0 r-reshape2@1.4.4 r-seuratobject@5.1.0 r-singlecellexperiment@1.30.1 r-stringr@1.5.1 r-summarizedexperiment@1.38.1 r-ucell@2.12.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/escape
Licenses: GPL 2
Synopsis: Single cell analysis platform for enrichment
Description:

R-escape streamlines gene set enrichment analysis for single-cell RNA sequencing. Using raw count information, Seurat objects, or SingleCellExperiment format, users can perform and visualize GSEA across individual cells.

r-catalyst 1.32.0
Propagated dependencies: r-circlize@0.4.16 r-complexheatmap@2.24.0 r-consensusclusterplus@1.72.0 r-cowplot@1.1.3 r-data-table@1.17.4 r-dplyr@1.1.4 r-drc@3.0-1 r-flowcore@2.20.0 r-flowsom@2.16.0 r-ggplot2@3.5.2 r-ggrepel@0.9.6 r-ggridges@0.5.6 r-gridextra@2.3 r-matrix@1.7-3 r-matrixstats@1.5.0 r-nnls@1.6 r-purrr@1.0.4 r-rcolorbrewer@1.1-3 r-reshape2@1.4.4 r-rtsne@0.17 r-s4vectors@0.46.0 r-scales@1.4.0 r-scater@1.36.0 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/HelenaLC/CATALYST
Licenses: GPL 2+
Synopsis: Cytometry data analysis tools
Description:

This package is Cytometry dATa anALYSis Tools (CATALYST). Mass cytometry like Cytometry by time of flight (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. CATALYST was designed to provide a pipeline for preprocessing of cytometry data, including:

  1. normalization using bead standards;

  2. single-cell deconvolution;

  3. bead-based compensation.

r-damefinder 1.20.0
Propagated dependencies: r-biocgenerics@0.54.0 r-biostrings@2.76.0 r-bumphunter@1.50.0 r-cowplot@1.1.3 r-genomeinfodb@1.44.0 r-genomicalignments@1.44.0 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-iranges@2.42.0 r-limma@3.64.1 r-plyr@1.8.9 r-readr@2.1.5 r-reshape2@1.4.4 r-rsamtools@2.24.0 r-s4vectors@0.46.0 r-stringr@1.5.1 r-summarizedexperiment@1.38.1 r-variantannotation@1.54.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/DAMEfinder
Licenses: Expat
Synopsis: Differential allelicly methylated regions
Description:

This package offers functionality for taking methtuple or Bismark outputs to calculate ASM scores and compute DAMEs regions. It also offers nice visualization of methyl-circle plots.

r-chipexoqualexample 1.32.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.github.com/keleslab/ChIPexoQualExample
Licenses: GPL 2+
Synopsis: Example data for the ChIPexoQual package
Description:

This package contains data for the ChIPexoQual package, consisting of 3 chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome.

r-rgadem 2.55.0
Propagated dependencies: r-biostrings@2.76.0 r-bsgenome@1.76.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-seqlogo@1.74.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/rGADEM/
Licenses: Artistic License 2.0
Synopsis: De novo sequence motif discovery
Description:

rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data.

r-pepsnmr 1.26.0
Propagated dependencies: r-ggplot2@3.5.2 r-gridextra@2.3 r-matrix@1.7-3 r-matrixstats@1.5.0 r-ptw@1.9-16 r-reshape2@1.4.4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ManonMartin/PepsNMR
Licenses: GPL 2
Synopsis: Pre-process 1H-NMR FID signals
Description:

This package provides R functions for common pre-processing steps that are applied on 1H-NMR data. It also provides a function to read the FID signals directly in the Bruker format.

r-rsubread 2.22.1
Dependencies: zlib@1.3.1
Propagated dependencies: r-matrix@1.7-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Rsubread/
Licenses: GPL 3
Synopsis: Subread sequence alignment and counting for R
Description:

This package provides tools for alignment, quantification and analysis of second and third generation sequencing data. It includes functionality for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and to both short and long sequence reads.

r-multidataset 1.36.0
Propagated dependencies: r-biobase@2.68.0 r-biocgenerics@0.54.0 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-ggrepel@0.9.6 r-iranges@2.42.0 r-limma@3.64.1 r-qqman@0.1.9 r-s4vectors@0.46.0 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MultiDataSet/
Licenses: Expat
Synopsis: Implementation of MultiDataSet and ResultSet
Description:

This package provides an implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages.

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Total results: 45109