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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-biocstyle 2.38.0
Propagated dependencies: r-biocmanager@1.30.27 r-bookdown@0.45 r-knitr@1.50 r-rmarkdown@2.30 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
Build system: r
Synopsis: Bioconductor formatting styles
Description:

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

r-mousegastrulationdata 1.24.0
Propagated dependencies: r-biocgenerics@0.56.0 r-bumpymatrix@1.18.0 r-experimenthub@3.0.0 r-s4vectors@0.48.0 r-singlecellexperiment@1.32.0 r-spatialexperiment@1.20.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/MarioniLab/MouseGastrulationData
Licenses: GPL 3
Build system: r
Synopsis: Single-Cell omics data across mouse gastrulation and early organogenesis
Description:

This package provides processed and raw count data for single-cell RNA sequencing. In addition, this package offers single-cell ATAC-seq, and seqFISH (spatial transcriptomic) experiments performed along a timecourse of mouse gastrulation and early organogenesis.

r-atena 1.16.0
Propagated dependencies: r-annotationhub@4.0.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-cli@3.6.5 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-matrix@1.7-4 r-matrixgenerics@1.22.0 r-matrixstats@1.5.0 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-sparsematrixstats@1.22.0 r-squarem@2021.1 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/functionalgenomics/atena
Licenses: Artistic License 2.0
Build system: r
Synopsis: Analysis of transposable elements
Description:

The atena package quantifies expression of TEs (transposable elements) from RNA-seq data through different methods, including ERVmap, TEtranscripts and Telescope. A common interface is provided to use each of these methods, which consists of building a parameter object, calling the quantification function with this object and getting a SummarizedExperiment object as an output container of the quantified expression profiles. The implementation allows quantifing TEs and gene transcripts in an integrated manner.

r-aims 1.42.0
Propagated dependencies: r-biobase@2.70.0 r-e1071@1.7-16
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://git.bioconductor.org/packages/AIMS
Licenses: Artistic License 2.0
Build system: r
Synopsis: Absolute assignment of breast cancer intrinsic molecular subtype
Description:

This package contains an implementation of AIMS -- Absolute Intrinsic Molecular Subtyping. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be done on individual samples as well as on dataset of gene expression data.

r-multidataset 1.38.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-iranges@2.44.0 r-limma@3.66.0 r-qqman@0.1.9 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/MultiDataSet/
Licenses: Expat
Build system: r
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.

r-basics 2.22.0
Propagated dependencies: r-assertthat@0.2.1 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-coda@0.19-4.1 r-cowplot@1.2.0 r-ggextra@0.11.0 r-ggplot2@4.0.1 r-hexbin@1.28.5 r-mass@7.3-65 r-matrix@1.7-4 r-matrixstats@1.5.0 r-posterior@1.6.1 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1 r-reshape2@1.4.5 r-s4vectors@0.48.0 r-scran@1.38.0 r-scuttle@1.20.0 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0 r-viridis@0.6.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/catavallejos/BASiCS
Licenses: GPL 3
Build system: r
Synopsis: Bayesian analysis of single-cell sequencing data
Description:

BASiCS is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments (where the groups of cells of interest are known a priori. BASiCS performs built-in data normalisation (global scaling) and technical noise quantification (based on spike-in genes). BASiCS provides an intuitive detection criterion for highly (or lowly) variable genes within a single group of cells. Additionally, BASiCS can compare gene expression patterns between two or more pre-specified groups of cells.

r-bsgenome-dmelanogaster-ucsc-dm3 1.4.0
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Fly
Description:

This package provides full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in Biostrings objects.

r-hybridmtest 1.54.0
Propagated dependencies: r-biobase@2.70.0 r-fdrtool@1.2.18 r-mass@7.3-65 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/HybridMTest
Licenses: GPL 2+
Build system: r
Synopsis: Hybrid multiple testing
Description:

This package performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using EBP estimates obtained by Grenander density estimation. For instance, for 3-group comparison analysis, Hybrid Multiple testing considers EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test of normality as weight. Instead of just using EBPs from F-test only or using H-test only, this methodology combines both types of EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses then the law of total EBPs.

r-scgate 1.7.2
Propagated dependencies: r-biocparallel@1.44.0 r-colorspace@2.1-2 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-ggridges@0.5.7 r-patchwork@1.3.2 r-reshape2@1.4.5 r-seurat@5.3.1 r-ucell@2.14.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/carmonalab/scGate
Licenses: GPL 3
Build system: r
Synopsis: Marker-based cell type purification for single-cell sequencing data
Description:

This package provides a method to purify a cell type or cell population of interest from heterogeneous datasets. scGate package automatizes marker-based purification of specific cell populations, without requiring training data or reference gene expression profiles. scGate takes as input a gene expression matrix stored in a Seurat object and a GM, consisting of a set of marker genes that define the cell population of interest. It evaluates the strength of signature marker expression in each cell using the rank-based method UCell, and then performs kNN smoothing by calculating the mean UCell score across neighboring cells. kNN-smoothing aims at compensating for the large degree of sparsity in scRNAseq data. Finally, a universal threshold over kNN-smoothed signature scores is applied in binary decision trees generated from the user-provided gating model, to annotate cells as either “pure” or “impure”, with respect to the cell population of interest.

r-asafe 1.36.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ASAFE
Licenses: Artistic License 2.0
Build system: r
Synopsis: Ancestry Specific Allele Frequency Estimation
Description:

The ASAFE package contains a collection of functions that can be used to carry out an EM (Expectation–maximization) algorithm to estimate ancestry-specific allele frequencies for a bi-allelic genetic marker, e.g. an SNP (single nucleotide polymorphism) from genotypes and ancestry pairs.

r-fishpond 2.16.0
Propagated dependencies: r-abind@1.4-8 r-genomicranges@1.62.0 r-gtools@3.9.5 r-iranges@2.44.0 r-jsonlite@2.0.0 r-matrix@1.7-4 r-matrixstats@1.5.0 r-qvalue@2.42.0 r-s4vectors@0.48.0 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0 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
Build system: r
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-biocsingular 1.26.1
Propagated dependencies: r-assorthead@1.4.0 r-beachmat@2.26.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-delayedarray@0.36.0 r-irlba@2.3.5.1 r-matrix@1.7-4 r-rcpp@1.1.0 r-rsvd@1.0.5 r-s4vectors@0.48.0 r-scaledmatrix@1.18.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/LTLA/BiocSingular
Licenses: GPL 3
Build system: r
Synopsis: Singular value decomposition for Bioconductor packages
Description:

This package implements exact and approximate methods for singular value decomposition and principal components analysis, in a framework that allows them to be easily switched within Bioconductor packages or workflows. Where possible, parallelization is achieved using the BiocParallel framework.

r-sparsematrixstats 1.22.0
Propagated dependencies: r-matrix@1.7-4 r-matrixgenerics@1.22.0 r-matrixstats@1.5.0 r-rcpp@1.1.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/sparseMatrixStats/
Licenses: Expat
Build system: r
Synopsis: Summary statistics for rows and columns of sparse matrices
Description:

This package provides high performance functions for row and column operations on sparse matrices. Currently, the optimizations are limited to data in the column sparse format.

r-biotip 1.24.0
Propagated dependencies: r-cluster@2.1.8.1 r-doparallel@1.0.17 r-foreach@1.5.2 r-genomicranges@1.62.0 r-igraph@2.2.1 r-mass@7.3-65 r-psych@2.5.6 r-scran@1.38.0 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/xyang2uchicago/BioTIP
Licenses: GPL 2
Build system: r
Synopsis: R package for characterization of biological tipping-point
Description:

This package adopts tipping-point theory to transcriptome profiles to help unravel disease regulatory trajectory.

r-rtcga-rnaseq 20151101.40.0
Propagated dependencies: r-rtcga@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/RTCGA.rnaseq
Licenses: GPL 2
Build system: r
Synopsis: Rna-seq datasets from The Cancer Genome Atlas Project
Description:

This package provides rna-seq datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. The Rna-seq data format is explained here https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2. The data source is Illumina hiseq Level 3 RSEM normalized expression data from 2015-11-01 snapshot.

r-rcy3 2.30.0
Propagated dependencies: r-base64enc@0.1-3 r-base64url@1.4 r-biocgenerics@0.56.0 r-fs@1.6.6 r-glue@1.8.0 r-gplots@3.2.0 r-graph@1.88.0 r-httr@1.4.7 r-irdisplay@1.1 r-irkernel@1.3.2 r-rcolorbrewer@1.1-3 r-rcurl@1.98-1.17 r-rjsonio@2.0.0 r-stringi@1.8.7 r-uuid@1.2-1 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/cytoscape/RCy3
Licenses: Expat
Build system: r
Synopsis: Functions to access and control Cytoscape
Description:

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

r-org-dr-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.Dr.eg.db/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation for Zebrafish
Description:

This package provides genome wide annotations for Zebrafish, primarily based on mapping using Entrez Gene identifiers.

r-zfpkm 1.32.0
Propagated dependencies: r-checkmate@2.3.3 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-summarizedexperiment@1.40.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ronammar/zFPKM/
Licenses: GPL 3
Build system: r
Synopsis: Functions to facilitate zFPKM transformations
Description:

This is a package to perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113).

r-gdsfmt 1.46.0
Dependencies: lz4@1.10.0 xz@5.4.5 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://corearray.sourceforge.net/
Licenses: LGPL 3
Build system: r
Synopsis: R Interface to CoreArray Genomic Data Structure (GDS) Files
Description:

This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.

r-aseb 1.54.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ASEB
Licenses: GPL 3+
Build system: r
Synopsis: Predict acetylated lysine sites
Description:

ASEB is an R package to predict lysine sites that can be acetylated by a specific KAT (K-acetyl-transferases) family. Lysine acetylation is a well-studied posttranslational modification on kinds of proteins. About four thousand lysine acetylation sites and over 20 lysine KATs have been identified. However, which KAT is responsible for a given protein or lysine site acetylation is mostly unknown. In this package, we use a GSEA-like (Gene Set Enrichment Analysis) method to make predictions. GSEA method was developed and successfully used to detect coordinated expression changes and find the putative functions of the long non-coding RNAs.

r-minfidata 0.56.0
Propagated dependencies: r-illuminahumanmethylation450kanno-ilmn12-hg19@0.6.1 r-illuminahumanmethylation450kmanifest@0.4.0 r-minfi@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/minfiData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Example data for the Illumina Methylation 450k array
Description:

This package provides data from 6 samples across 2 groups from 450k methylation arrays.

r-basic4cseq 1.46.0
Propagated dependencies: r-biostrings@2.78.0 r-bsgenome-ecoli-ncbi-20080805@1.3.1000 r-catools@1.18.3 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-rcircos@1.2.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Basic4Cseq
Licenses: LGPL 3
Build system: r
Synopsis: Analyzing 4C-seq data
Description:

Basic4Cseq is an R package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

r-bcellviper 1.46.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/bcellViper
Licenses: GPL 2+
Build system: r
Synopsis: Transcriptional interactome and normal human B-cell expression data
Description:

This is a tool for human B-cell context-specific transcriptional regulatory network. In addition, this package provides a human normal B-cells dataset for the examples in package viper.

r-seqpattern 1.42.0
Propagated dependencies: r-biostrings@2.78.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-kernsmooth@2.23-26 r-plotrix@3.8-13
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/seqPattern
Licenses: GPL 3+
Build system: r
Synopsis: Visualising oligonucleotide patterns and motif occurrences
Description:

This package provides tools to visualize oligonucleotide patterns and sequence motif occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.

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Total results: 69112