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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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where search is your query, page is a page number and limit is a number of items on a single page. Pagination information (such as a number of pages and etc) is returned in response headers.

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r-flowviz 1.74.0
Propagated dependencies: r-biobase@2.70.0 r-flowcore@2.22.0 r-hexbin@1.28.5 r-idpmisc@1.1.21 r-kernsmooth@2.23-26 r-lattice@0.22-7 r-latticeextra@0.6-31 r-mass@7.3-65 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/flowViz/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Visualization for flow cytometry
Description:

This package provides visualization tools for flow cytometry data.

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-agilp 3.42.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/agilp
Licenses: GPL 3
Build system: r
Synopsis: Processing of Agilent expression array
Description:

This package aims to provide a pipeline for the low-level analysis of gene expression microarray data, primarily focused on the Agilent platform, but which also provides utilities which may be useful for other platforms.

r-phastcons100way-ucsc-hg19 3.7.2
Propagated dependencies: r-bsgenome@1.78.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-genomicscores@2.22.0 r-iranges@2.44.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/phastCons100way.UCSC.hg19
Licenses: Artistic License 2.0
Build system: r
Synopsis: UCSC phastCons conservation scores for hg19
Description:

This package provides UCSC phastCons conservation scores for the human genome (hg19) calculated from multiple alignments with other 99 vertebrate species.

r-structuralvariantannotation 1.26.0
Propagated dependencies: r-assertthat@0.2.1 r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-dplyr@1.1.4 r-genomeinfodb@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-pwalign@1.6.0 r-rlang@1.1.6 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/StructuralVariantAnnotation/
Licenses: GPL 3
Build system: r
Synopsis: R package designed to simplify structural variant analysis
Description:

This package contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

r-mlinterfaces 1.90.0
Propagated dependencies: r-annotate@1.88.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-cluster@2.1.8.1 r-fpc@2.2-13 r-gbm@2.2.2 r-gdata@3.0.1 r-genefilter@1.92.0 r-ggvis@0.4.9 r-hwriter@1.3.2.1 r-magrittr@2.0.4 r-mass@7.3-65 r-mlbench@2.1-6 r-pls@2.8-5 r-rcolorbrewer@1.1-3 r-rcpp@1.1.0 r-rpart@4.1.24 r-sfsmisc@1.1-23 r-shiny@1.11.1 r-summarizedexperiment@1.40.0 r-threejs@0.3.4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MLInterfaces/
Licenses: LGPL 2.1+
Build system: r
Synopsis: Interfaces to R machine learning procedures
Description:

This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.

r-trnadbimport 1.28.0
Propagated dependencies: r-biostrings@2.78.0 r-genomicranges@1.62.0 r-httr2@1.2.1 r-iranges@2.44.0 r-modstrings@1.26.0 r-s4vectors@0.48.0 r-stringr@1.6.0 r-structstrings@1.26.0 r-trna@1.28.0 r-xml2@1.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/tRNAdbImport
Licenses: GPL 3
Build system: r
Synopsis: Importing from tRNAdb and mitotRNAdb as GRanges objects
Description:

tRNAdbImport imports the entries of the tRNAdb and mtRNAdb as GRanges object.

r-celldex 1.20.0
Propagated dependencies: r-alabaster-base@1.10.0 r-alabaster-matrix@1.10.0 r-alabaster-se@1.10.0 r-annotationdbi@1.72.0 r-annotationhub@4.0.0 r-dbi@1.2.3 r-delayedarray@0.36.0 r-delayedmatrixstats@1.32.0 r-experimenthub@3.0.0 r-gypsum@1.6.0 r-jsonlite@2.0.0 r-matrix@1.7-4 r-rsqlite@2.4.4 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/LTLA/celldex
Licenses: GPL 3
Build system: r
Synopsis: Reference index for cell types
Description:

This package provides a collection of reference expression datasets with curated cell type labels, for use in procedures like automated annotation of single-cell data or deconvolution of bulk RNA-seq.

r-sva 3.58.0
Propagated dependencies: r-biocparallel@1.44.0 r-edger@4.8.0 r-genefilter@1.92.0 r-limma@3.66.0 r-matrixstats@1.5.0 r-mgcv@1.9-4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/sva
Licenses: Artistic License 2.0
Build system: r
Synopsis: Surrogate variable analysis
Description:

This package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. It also contains functions for identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data like gene expression/RNA sequencing/methylation/brain imaging data that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise.

r-motifstack 1.54.0
Propagated dependencies: r-ade4@1.7-23 r-biostrings@2.78.0 r-ggplot2@4.0.1 r-htmlwidgets@1.6.4 r-tfbstools@1.48.0 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/motifStack/
Licenses: GPL 2+
Build system: r
Synopsis: Plot stacked logos for DNA, RNA and amino acid sequences
Description:

The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motifs and amino acid sequence motifs. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.

r-pfam-db 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/PFAM.db
Licenses: Artistic License 2.0
Build system: r
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-aucell 1.32.0
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-delayedarray@0.36.0 r-delayedmatrixstats@1.32.0 r-gseabase@1.72.0 r-matrix@1.7-4 r-mixtools@2.0.0.1 r-r-utils@2.13.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AUCell/
Licenses: GPL 3
Build system: r
Synopsis: Analysis of gene set activity in single-cell RNA-seq data
Description:

AUCell identifies cells with active gene sets (e.g. signatures, gene modules, etc) in single-cell RNA-seq data. AUCell uses the Area Under the Curve (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.

r-scistreer 1.2.0
Propagated dependencies: r-ape@5.8-1 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-ggtree@4.0.1 r-igraph@2.2.1 r-paralleldist@0.2.7 r-patchwork@1.3.2 r-phangorn@2.12.1 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1 r-rcppparallel@5.1.11-1 r-reshape2@1.4.5 r-rhpcblasctl@0.23-42 r-stringr@1.6.0 r-tidygraph@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/kharchenkolab/scistreer
Licenses: GPL 3
Build system: r
Synopsis: Maximum-likelihood perfect phylogeny Inference at scale
Description:

This package provides fast maximum-likelihood phylogeny inference from noisy single-cell data using the ScisTree algorithm proposed by doi.org/10.1093/bioinformatics/btz676, Yufeng Wu (2019). It makes the method applicable to massive single-cell datasets (>10,000 cells).

r-bags 2.50.0
Propagated dependencies: r-biobase@2.70.0 r-breastcancervdx@1.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BAGS
Licenses: Artistic License 2.0
Build system: r
Synopsis: Bayesian approach for geneset selection
Description:

This R package is providing functions to perform geneset significance analysis over simple cross-sectional data between 2 and 5 phenotypes of interest.

r-bumphunter 1.52.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biocgenerics@0.56.0 r-dorng@1.8.6.2 r-foreach@1.5.2 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-iterators@1.0.14 r-limma@3.66.0 r-locfit@1.5-9.12 r-matrixstats@1.5.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ririzarr/bumphunter
Licenses: Artistic License 2.0
Build system: r
Synopsis: Find bumps in genomic data
Description:

This package provides tools for finding bumps in genomic data in order to identify differentially methylated regions in epigenetic epidemiology studies.

r-tkwidgets 1.88.0
Propagated dependencies: r-dyndoc@1.88.0 r-widgettools@1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/tkWidgets
Licenses: Artistic License 2.0
Build system: r
Synopsis: R based tk widgets
Description:

This package implements widgets to provide user interfaces.

r-copyhelper 1.42.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/CopyhelpeR/
Licenses: GPL 2
Build system: r
Synopsis: Helper files for CopywriteR
Description:

This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display copy number variation. Files are stored as GRanges objects from the GenomicRanges Bioconductor package.

r-biocparallel 1.44.0
Propagated dependencies: r-bh@1.87.0-1 r-codetools@0.2-20 r-cpp11@0.5.2 r-futile-logger@1.4.3 r-snow@0.4-4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BiocParallel
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: Bioconductor facilities for parallel evaluation
Description:

This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

r-fcscan 1.24.0
Propagated dependencies: r-doparallel@1.0.17 r-foreach@1.5.2 r-genomicranges@1.62.0 r-iranges@2.44.0 r-plyr@1.8.9 r-rtracklayer@1.70.0 r-summarizedexperiment@1.40.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/fcScan
Licenses: Artistic License 2.0
Build system: r
Synopsis: Detect clusters of coordinates with user defined options
Description:

This package is used to detect combination of genomic coordinates falling within a user defined window size along with user defined overlap between identified neighboring clusters. It can be used for genomic data where the clusters are built on a specific chromosome or specific strand. Clustering can be performed with a "greedy" option allowing thus the presence of additional sites within the allowed window size.

r-ihw 1.38.0
Propagated dependencies: r-biocgenerics@0.56.0 r-fdrtool@1.2.18 r-lpsymphony@1.38.0 r-slam@0.1-55
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/IHW
Licenses: Artistic License 2.0
Build system: r
Synopsis: Independent hypothesis weighting
Description:

Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.

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-affydata 1.58.0
Propagated dependencies: r-affy@1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/affydata/
Licenses: GPL 2+
Build system: r
Synopsis: Affymetrix data for demonstration purposes
Description:

This package provides example datasets that represent 'real world examples' of Affymetrix data, unlike the artificial examples included in the package affy.

r-chemminer 3.62.0
Propagated dependencies: r-base64enc@0.1-3 r-bh@1.87.0-1 r-biocgenerics@0.56.0 r-dbi@1.2.3 r-digest@0.6.39 r-dt@0.34.0 r-ggplot2@4.0.1 r-gridextra@2.3 r-jsonlite@2.0.0 r-png@0.1-8 r-rcpp@1.1.0 r-rcurl@1.98-1.17 r-rjson@0.2.23 r-rsvg@2.7.0 r-stringi@1.8.7
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/girke-lab/ChemmineR
Licenses: Artistic License 2.0
Build system: r
Synopsis: Cheminformatics toolkit for R
Description:

ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. It contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.

r-zlibbioc 1.54.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/zlibbioc
Licenses: Artistic License 2.0
Build system: r
Synopsis: Provider for zlib-1.2.5 to R packages
Description:

This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means.

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Total results: 69112