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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:

GET /api/packages?search=hello&page=1&limit=20

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-snplocs-hsapiens-dbsnp144-grch37 0.99.20
Propagated dependencies: r-biocgenerics@0.56.0 r-bsgenome@1.78.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 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/SNPlocs.Hsapiens.dbSNP144.GRCh37/
Licenses: Artistic License 2.0
Build system: r
Synopsis: SNP locations for Homo sapiens (dbSNP Build 144)
Description:

This package provides SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be injected in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).

r-xina 1.28.0
Propagated dependencies: r-alluvial@0.1-2 r-ggplot2@4.0.1 r-gridextra@2.3 r-igraph@2.2.1 r-mclust@6.1.2 r-plyr@1.8.9 r-stringdb@2.22.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://git.bioconductor.org/packages/XINA
Licenses: GPL 3
Build system: r
Synopsis: Identifying proteins that exhibit similar patterns
Description:

The aim of XINA is to determine which proteins exhibit similar patterns within and across experimental conditions, since proteins with co-abundance patterns may have common molecular functions. XINA imports multiple datasets, tags dataset in silico, and combines the data for subsequent subgrouping into multiple clusters. The result is a single output depicting the variation across all conditions. XINA not only extracts coabundance profiles within and across experiments, but also incorporates protein-protein interaction databases and integrative resources such as Kyoto encyclopedia of genes and genomes (KEGG) to infer interactors and molecular functions, respectively, and produces intuitive graphical outputs.

r-annotationdbi 1.72.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-dbi@1.2.3 r-iranges@2.44.0 r-keggrest@1.50.0 r-rsqlite@2.4.4 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AnnotationDbi
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation database interface
Description:

This package provides user interface and database connection code for annotation data packages using SQLite data storage.

r-bgeedb 2.36.0
Propagated dependencies: r-anndata@0.8.0 r-biobase@2.70.0 r-bread@0.4.1 r-curl@7.0.0 r-data-table@1.17.8 r-digest@0.6.39 r-dplyr@1.1.4 r-graph@1.88.0 r-hdf5array@1.38.0 r-r-utils@2.13.0 r-rcurl@1.98-1.17 r-rsqlite@2.4.4 r-tidyr@1.3.1 r-topgo@2.62.0 r-zellkonverter@1.20.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/BgeeDB/BgeeDB_R
Licenses: GPL 3
Build system: r
Synopsis: Annotation and gene expression data retrieval from Bgee database
Description:

This package provides a package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.

r-systempiper 2.16.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-crayon@1.5.3 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-htmlwidgets@1.6.4 r-magrittr@2.0.4 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-shortread@1.68.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/tgirke/systemPipeR
Licenses: Artistic License 2.0
Build system: r
Synopsis: Next generation sequencing workflow and reporting environment
Description:

This R package provides tools for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure.

r-cycombine 0.2.6-1.f18504b
Propagated dependencies: r-biobase@2.70.0 r-cytolib@2.22.0 r-dplyr@1.1.4 r-flowcore@2.22.0 r-ggplot2@4.0.1 r-knitr@1.50 r-kohonen@3.0.12 r-magrittr@2.0.4 r-purrr@1.2.0 r-rcolorbrewer@1.1-3 r-readr@2.1.6 r-readxl@1.4.5 r-stringr@1.6.0 r-sva@3.58.0 r-tibble@3.3.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/biosurf/cyCombine
Licenses: Expat
Build system: r
Synopsis: Integration of single-cell cytometry datasets
Description:

This package provides a method for combining single-cell cytometry datasets, which increases the analytical flexibility and the statistical power of the analyses while minimizing technical noise.

r-mbkmeans 1.26.0
Propagated dependencies: r-beachmat@2.26.0 r-benchmarkme@1.0.8 r-biocparallel@1.44.0 r-clusterr@1.3.5 r-delayedarray@0.36.0 r-matrix@1.7-4 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1 r-rhdf5lib@1.32.0 r-s4vectors@0.48.0 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/mbkmeans
Licenses: Expat
Build system: r
Synopsis: Mini-batch k-means clustering for single-cell RNA-seq
Description:

This package implements the mini-batch k-means algorithm for large datasets, including support for on-disk data representation.

r-anf 1.32.0
Propagated dependencies: r-biobase@2.70.0 r-igraph@2.2.1 r-mass@7.3-65 r-rcolorbrewer@1.1-3 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ANF
Licenses: GPL 3
Build system: r
Synopsis: Affinity network fusion for complex patient clustering
Description:

The package ANF(Affinity Network Fusion) provides methods for affinity matrix construction and fusion as well as spectral clustering. This package is used for complex patient clustering by integrating multi-omic data through affinity network fusion.

r-flowclust 3.48.0
Dependencies: gsl@2.8
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-flowcore@2.22.0 r-graph@1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/flowClust
Licenses: Artistic License 2.0
Build system: r
Synopsis: Clustering for flow cytometry
Description:

This package provides robust model-based clustering using a t-mixture model with Box-Cox transformation.

r-beclear 2.26.0
Propagated dependencies: r-abind@1.4-8 r-biocparallel@1.44.0 r-data-table@1.17.8 r-dixontest@1.0.4 r-futile-logger@1.4.3 r-ids@1.0.1 r-matrix@1.7-4 r-rcpp@1.1.0 r-rdpack@2.6.4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/uds-helms/BEclear
Licenses: GPL 3
Build system: r
Synopsis: Correction of batch effects in DNA methylation data
Description:

This package provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

r-rgraphviz 2.54.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-graph@1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Rgraphviz
Licenses: EPL 1.0
Build system: r
Synopsis: Plotting capabilities for R graph objects
Description:

This package interfaces R with the graphviz library for plotting R graph objects from the graph package.

r-bacon 1.38.0
Propagated dependencies: r-biocparallel@1.44.0 r-ellipse@0.5.0 r-ggplot2@4.0.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/bacon/
Licenses: GPL 2+
Build system: r
Synopsis: Controlling bias and inflation in association studies
Description:

Bacon can be used to remove inflation and bias often observed in epigenome- and transcriptome-wide association studies. To this end bacon constructs an empirical null distribution using a Gibbs Sampling algorithm by fitting a three-component normal mixture on z-scores.

r-cytoml 2.22.0
Dependencies: libxml2@2.14.6 zlib@1.3.1
Propagated dependencies: r-bh@1.87.0-1 r-biobase@2.70.0 r-cpp11@0.5.2 r-cytolib@2.22.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-flowcore@2.22.0 r-flowworkspace@4.22.0 r-ggcyto@1.38.0 r-graph@1.88.0 r-jsonlite@2.0.0 r-opencyto@2.22.0 r-rbgl@1.86.0 r-rgraphviz@2.54.0 r-rhdf5lib@1.32.0 r-rprotobuflib@2.22.0 r-tibble@3.3.0 r-xml@3.99-0.20 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/RGLab/CytoML
Licenses: Artistic License 2.0
Build system: r
Synopsis: GatingML interface for cross platform cytometry data sharing
Description:

This package provides an interface to implementations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.

r-biomvrcns 1.50.0
Propagated dependencies: r-genomicranges@1.62.0 r-gviz@1.54.0 r-iranges@2.44.0 r-mvtnorm@1.3-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/biomvRCNS
Licenses: GPL 2+
Build system: r
Synopsis: Copy number study and segmentation for multivariate biological data
Description:

In this package, a Hidden Semi Markov Model (HSMM) and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing.

r-dada2 1.38.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-rcpp@1.1.0 r-rcppparallel@5.1.11-1 r-reshape2@1.4.5 r-shortread@1.68.0 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://benjjneb.github.io/dada2/
Licenses: LGPL 2.0
Build system: r
Synopsis: Accurate, high-resolution sample inference from amplicon sequencing data
Description:

The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.

r-bionetstat 1.22.0
Propagated dependencies: r-biocparallel@1.44.0 r-dt@0.34.0 r-ggplot2@4.0.1 r-hmisc@5.2-4 r-igraph@2.2.1 r-knitr@1.50 r-markdown@2.0 r-pathview@1.50.0 r-pheatmap@1.0.13 r-plyr@1.8.9 r-psych@2.5.6 r-rcolorbrewer@1.1-3 r-rjsonio@2.0.0 r-rmarkdown@2.30 r-shiny@1.11.1 r-shinybs@0.61.1 r-whisker@0.4.1 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/jardimViniciusC/BioNetStat
Licenses: GPL 3+
Build system: r
Synopsis: Biological network analysis
Description:

This package provides a package to perform differential network analysis, differential node analysis (differential coexpression analysis), network and metabolic pathways view.

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-hgu133plus2-db 3.13.0
Propagated dependencies: r-annotationdbi@1.72.0 r-org-hs-eg-db@3.22.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/hgu133plus2.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix HG-U133_Plus_2 Array annotation data
Description:

This package provides Affymetrix HG-U133_Plus_2 array annotation data (chip hgu133plus2) assembled using data from public repositories.

r-ggtreeextra 1.20.0
Propagated dependencies: r-cli@3.6.5 r-ggnewscale@0.5.2 r-ggplot2@4.0.1 r-ggtree@4.0.1 r-magrittr@2.0.4 r-rlang@1.1.6 r-tidytree@0.4.6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/YuLab-SMU/ggtreeExtra/
Licenses: GPL 3+
Build system: r
Synopsis: Add geometric layers On circular or other layout tree of ggtree
Description:

ggtreeExtra extends the method for mapping and visualizing associated data on phylogenetic tree using ggtree. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by ggtree with the grammar of ggplot2.

r-chicago 1.38.0
Propagated dependencies: r-data-table@1.17.8 r-delaporte@8.4.2 r-hmisc@5.2-4 r-mass@7.3-65 r-matrixstats@1.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Chicago
Licenses: Artistic License 2.0
Build system: r
Synopsis: Capture Hi-C analysis of genomic organization
Description:

This package provides a pipeline for analysing Capture Hi-C data.

r-cicero-monocle3 1.3.9-1.495ef0d
Propagated dependencies: r-monocle3@1.3.7-1.98402ed r-assertthat@0.2.1 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-fnn@1.1.4.1 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-glasso@1.11 r-gviz@1.54.0 r-igraph@2.2.1 r-iranges@2.44.0 r-matrix@1.7-4 r-plyr@1.8.9 r-reshape2@1.4.5 r-s4vectors@0.48.0 r-stringi@1.8.7 r-stringr@1.6.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-vgam@1.1-13
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/cicero/
Licenses: Expat
Build system: r
Synopsis: Predict cis-co-accessibility from single-cell data
Description:

Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends the monocle package for use in chromatin accessibility data.

r-quantsmooth 1.76.0
Propagated dependencies: r-quantreg@6.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/quantsmooth
Licenses: GPL 2
Build system: r
Synopsis: Quantile smoothing and genomic visualization of array data
Description:

This package implements quantile smoothing. It contains a dataset used to produce human chromosomal ideograms for plotting purposes and a collection of arrays that contains data of chromosome 14 of 3 colorectal tumors. The package provides functions for painting chromosomal icons, chromosome or chromosomal idiogram and other types of plots. Quantsmooth offers options like converting chromosomal ids to their numeric form, retrieving the human chromosomal length from NCBI data, retrieving regions of interest in a vector of intensities using quantile smoothing, determining cytoband position based on the location of the probe, and other useful tools.

r-interactionset 1.38.0
Propagated dependencies: r-biocgenerics@0.56.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-matrix@1.7-4 r-rcpp@1.1.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/InteractionSet
Licenses: GPL 3
Build system: r
Synopsis: Base classes for storing genomic interaction data
Description:

This package provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.

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