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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:

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r-txdb-hsapiens-ucsc-hg38-knowngene 3.22.0
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.Hsapiens.UCSC.hg38.knownGene/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for human genome in TxDb format
Description:

This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg38 genome and based on the "knownGene" track. The database is exposed as a TxDb object.

r-triform 1.29.0
Propagated dependencies: r-biocgenerics@0.56.0 r-iranges@2.44.0 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/triform/
Licenses: GPL 2
Build system: r
Synopsis: Find enriched regions in transcription factor ChIP-sequencing data
Description:

The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.

r-altcdfenvs 2.72.0
Propagated dependencies: r-affy@1.88.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-hypergraph@1.82.0 r-makecdfenv@1.86.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/altcdfenvs
Licenses: GPL 2+
Build system: r
Synopsis: Convenience data structures and functions to handle CDF environments
Description:

The package is usable with Affymetrix GeneChip short oligonucleotide arrays, and it can be adapted or extended to other platforms. It is able to modify or replace the grouping of probes in the probe sets. Also, the package contains simple functions to read R connections in the FASTA format and it can create an alternative mapping from sequences.

r-glimma 2.20.0
Propagated dependencies: r-deseq2@1.50.2 r-edger@4.8.0 r-htmlwidgets@1.6.4 r-jsonlite@2.0.0 r-limma@3.66.0 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/Shians/Glimma
Licenses: LGPL 3
Build system: r
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-ebseq 2.8.0
Propagated dependencies: r-bh@1.87.0-1 r-blockmodeling@1.1.8 r-gplots@3.2.0 r-rcpp@1.1.0 r-rcppeigen@0.3.4.0.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/EBSeq
Licenses: Artistic License 2.0
Build system: r
Synopsis: Differential expression analysis of RNA-seq data
Description:

This package provides tools for differential expression analysis at both gene and isoform level using RNA-seq data

r-bsgenome-hsapiens-ucsc-hg38 1.4.5
Propagated dependencies: r-bsgenome@1.78.0 r-genomeinfodb@1.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Homo sapiens
Description:

This package provides full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.

r-residualmatrix 1.20.0
Propagated dependencies: r-delayedarray@0.36.0 r-matrix@1.7-4 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/LTLA/ResidualMatrix
Licenses: GPL 3
Build system: r
Synopsis: Create a DelayedMatrix of regression residuals
Description:

This package implements tools for delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. It also supports partial computation of residuals where selected factors are to be preserved in the output matrix. It implements a number of efficient methods for operating on the delayed matrix of residuals, most notably matrix multiplication and calculation of row/column sums or means.

r-zellkonverter 1.20.0
Propagated dependencies: r-basilisk@1.22.0 r-cli@3.6.5 r-delayedarray@0.36.0 r-matrix@1.7-4 r-reticulate@1.44.1 r-s4vectors@0.48.0 r-singlecellexperiment@1.32.0 r-sparsearray@1.10.2 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/theislab/zellkonverter
Licenses: Expat
Build system: r
Synopsis: Conversion between AnnData and single-cell experiments objects
Description:

This package provides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes functions to read and write H5AD files used for saving AnnData objects to disk.

r-badregionfinder 1.38.0
Propagated dependencies: r-biomart@2.66.0 r-genomicranges@1.62.0 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BadRegionFinder
Licenses: LGPL 3
Build system: r
Synopsis: Identifying regions with bad coverage in sequence alignment data
Description:

BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.

r-champdata 2.42.0
Propagated dependencies: r-biocgenerics@0.56.0 r-genomicranges@1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ChAMPdata
Licenses: GPL 3
Build system: r
Synopsis: Data packages for ChAMP package
Description:

This package provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis.

r-yamss 1.36.0
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-ebimage@4.52.0 r-iranges@2.44.0 r-limma@3.66.0 r-matrix@1.7-4 r-mzr@2.44.0 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/hansenlab/yamss
Licenses: Artistic License 2.0
Build system: r
Synopsis: Tools for high-throughput metabolomics
Description:

This package provides tools to analyze and visualize high-throughput metabolomics data acquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.

r-ioniser 2.34.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biostrings@2.78.0 r-bit64@4.6.0-1 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-magrittr@2.0.4 r-rhdf5@2.54.0 r-shortread@1.68.0 r-stringr@1.6.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/IONiseR/
Licenses: Expat
Build system: r
Synopsis: Quality assessment tools for Oxford Nanopore MinION data
Description:

IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.

r-isva 1.9
Propagated dependencies: r-fastica@1.2-7 r-jade@2.0-4 r-qvalue@2.42.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/package=isva
Licenses: GPL 2
Build system: r
Synopsis: Independent surrogate variable analysis
Description:

Independent Surrogate Variable Analysis is an algorithm for feature selection in the presence of potential confounding factors (see Teschendorff AE et al 2011, <doi: 10.1093/bioinformatics/btr171>).

r-seqbias 1.50.0
Propagated dependencies: r-biostrings@2.78.0 r-genomicranges@1.62.0 r-rhtslib@3.6.0 r-zlibbioc@1.54.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/seqbias/
Licenses: LGPL 3
Build system: r
Synopsis: Estimation of per-position bias in high-throughput sequencing data
Description:

This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.

r-mafh5-gnomad-v3-1-2-grch38 3.15.1
Propagated dependencies: r-bsgenome@1.78.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-genomicscores@2.22.0 r-hdf5array@1.38.0 r-iranges@2.44.0 r-rhdf5@2.54.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MafH5.gnomAD.v3.1.2.GRCh38
Licenses: Artistic License 2.0
Build system: r
Synopsis: Minor allele frequency data from gnomAD version 3.1.2 for GRCh38
Description:

This package is designed to store minor allele frequency data. It retrieves this data from the Genome Aggregation Database (gnomAD version 3.1.2) for the human genome version GRCh38.

r-fmcsr 1.52.0
Propagated dependencies: r-biocgenerics@0.56.0 r-chemminer@3.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/girke-lab/fmcsR
Licenses: Artistic License 2.0
Build system: r
Synopsis: Mismatch tolerant maximum common substructure searching
Description:

The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.

r-allelicimbalance 1.48.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-bsgenome@1.78.0 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-gridextra@2.3 r-gviz@1.54.0 r-iranges@2.44.0 r-lattice@0.22-7 r-latticeextra@0.6-31 r-nlme@3.1-168 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-seqinr@4.2-36 r-summarizedexperiment@1.40.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/pappewaio/AllelicImbalance
Licenses: GPL 3
Build system: r
Synopsis: Investigate allele-specific expression
Description:

This package provides a framework for allele-specific expression investigation using RNA-seq data.

r-awfisher 1.24.0
Propagated dependencies: r-edger@4.8.0 r-limma@3.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AWFisher
Licenses: GPL 3
Build system: r
Synopsis: Fast computing for adaptively weighted fisher's method
Description:

This package is an implementation of the Adaptively Weighted Fisher's method, including fast p-value computing, variability index, and meta-pattern.

r-bsgenome-mmusculus-ucsc-mm9 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.Mmusculus.UCSC.mm9/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Mouse
Description:

This package provides full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, July 2007) and stored in Biostrings objects.

r-bluster 1.20.0
Propagated dependencies: r-assorthead@1.4.0 r-biocneighbors@2.4.0 r-biocparallel@1.44.0 r-cluster@2.1.8.1 r-igraph@2.2.1 r-matrix@1.7-4 r-rcpp@1.1.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/bluster
Licenses: GPL 3
Build system: r
Synopsis: Clustering algorithms for Bioconductor
Description:

This package wraps common clustering algorithms in an easily extended S4 framework. Backends are implemented for hierarchical, k-means and graph-based clustering. Several utilities are also provided to compare and evaluate clustering results.

r-gqtlbase 1.21.1
Propagated dependencies: r-batchjobs@1.10 r-bbmisc@1.13 r-biocgenerics@0.56.0 r-bit@4.6.0 r-doparallel@1.0.17 r-ff@4.5.2 r-ffbase@0.13.3 r-foreach@1.5.2 r-genomicfiles@1.46.0 r-genomicranges@1.62.0 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://bioconductor.org/packages/gQTLBase
Licenses: Artistic License 2.0
Build system: r
Synopsis: Infrastructure for eQTL, mQTL and similar studies
Description:

The purpose of this package is to simplify the storage and interrogation of quantitative trait loci (QTL) archives, such as eQTL, mQTL, dsQTL, and more.

r-pcatools 2.20.0
Propagated dependencies: r-beachmat@2.26.0 r-bh@1.87.0-1 r-biocparallel@1.44.0 r-biocsingular@1.26.1 r-cowplot@1.2.0 r-delayedarray@0.36.0 r-delayedmatrixstats@1.32.0 r-dqrng@0.4.1 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-lattice@0.22-7 r-matrix@1.7-4 r-rcpp@1.1.0 r-reshape2@1.4.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/kevinblighe/PCAtools
Licenses: GPL 3
Build system: r
Synopsis: PCAtools: everything Principal Components Analysis
Description:

Principal Component Analysis (PCA) extracts the fundamental structure of the data without the need to build any model to represent it. This "summary" of the data is arrived at through a process of reduction that can transform the large number of variables into a lesser number that are uncorrelated (i.e. the 'principal components'), while at the same time being capable of easy interpretation on the original data. PCAtools provides functions for data exploration via PCA, and allows the user to generate publication-ready figures. PCA is performed via BiocSingular; users can also identify an optimal number of principal components via different metrics, such as the elbow method and Horn's parallel analysis, which has relevance for data reduction in single-cell RNA-seq (scRNA-seq) and high dimensional mass cytometry data.

r-interactivedisplaybase 1.48.0
Propagated dependencies: r-biocgenerics@0.56.0 r-dt@0.34.0 r-shiny@1.11.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/interactiveDisplayBase
Licenses: Artistic License 2.0
Build system: r
Synopsis: Base package for web displays of Bioconductor objects
Description:

This package contains the basic methods needed to generate interactive Shiny-based display methods for Bioconductor objects.

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.

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Total results: 68655