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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.

If you'd like to join our channel webring send a patch to ~whereiseveryone/toys@lists.sr.ht adding your channel as an entry in channels.scm.


r-org-ce-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.Ce.eg.db/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Genome wide annotation for Worm
Description:

This package provides mappings from Entrez gene identifiers to various annotations for the genome of the model worm Caenorhabditis elegans.

r-microbiomestat 1.2
Propagated dependencies: r-foreach@1.5.2 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-lmertest@3.1-3 r-mass@7.3-65 r-matrix@1.7-4 r-matrixstats@1.5.0 r-modeest@2.4.0 r-statmod@1.5.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/package=MicrobiomeStat
Licenses: GPL 3
Build system: r
Synopsis: Statistical methods for microbiome compositional data
Description:

This package provides a suite of methods for powerful and robust microbiome data analysis addressing zero-inflation, phylogenetic structure and compositional effects. The methods can be applied to the analysis of other (high-dimensional) compositional data arising from sequencing experiments.

r-mfuzz 2.70.0
Propagated dependencies: r-biobase@2.70.0 r-e1071@1.7-16 r-tkwidgets@1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://mfuzz.sysbiolab.eu/
Licenses: GPL 2
Build system: r
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-geoquery 2.78.0
Propagated dependencies: r-biobase@2.70.0 r-curl@7.0.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-httr2@1.2.1 r-limma@3.66.0 r-magrittr@2.0.4 r-r-utils@2.13.0 r-readr@2.1.6 r-rentrez@1.2.4 r-rvest@1.0.5 r-s4vectors@0.48.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-tidyr@1.3.1 r-xml2@1.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/seandavi/GEOquery/
Licenses: GPL 2
Build system: r
Synopsis: Get data from NCBI Gene Expression Omnibus (GEO)
Description:

The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.

r-flowsom 2.18.0
Propagated dependencies: r-biocgenerics@0.56.0 r-colorramps@2.3.4 r-consensusclusterplus@1.74.0 r-dplyr@1.1.4 r-flowcore@2.22.0 r-ggforce@0.5.0 r-ggnewscale@0.5.2 r-ggplot2@4.0.1 r-ggpubr@0.6.2 r-igraph@2.2.1 r-magrittr@2.0.4 r-rlang@1.1.6 r-rtsne@0.17 r-tidyr@1.3.1 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/FlowSOM/
Licenses: GPL 2+
Build system: r
Synopsis: Visualize and interpret cytometry data
Description:

FlowSOM offers visualization options for cytometry data, by using self-organizing map clustering and minimal spanning trees.

r-manor 1.82.0
Propagated dependencies: r-glad@2.74.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://bioinfo.curie.fr/projects/manor/index.html
Licenses: GPL 2
Build system: r
Synopsis: CGH micro-array normalization
Description:

This package ofers functions for importation, normalization, visualization, and quality control to correct identified sources of variability in array of CGH experiments.

r-timeseriesexperiment 1.13.0
Propagated dependencies: r-deseq2@1.50.2 r-dplyr@1.1.4 r-dynamictreecut@1.63-1 r-edger@4.8.0 r-ggplot2@4.0.1 r-hmisc@5.2-4 r-limma@3.66.0 r-magrittr@2.0.4 r-proxy@0.4-27 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-vegan@2.7-2 r-viridis@0.6.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/nlhuong/TimeSeriesExperiment/
Licenses: LGPL 3+
Build system: r
Synopsis: Analysis for short time-series data
Description:

This package is a visualization and analysis toolbox for short time course data which includes dimensionality reduction, clustering, two-sample differential expression testing and gene ranking techniques. The package also provides methods for retrieving enriched pathways.

r-methylclockdata 1.18.0
Propagated dependencies: r-experimenthub@3.0.0 r-experimenthubdata@1.36.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/isglobal-brge/methylclockData
Licenses: Expat
Build system: r
Synopsis: Data for methylclock package
Description:

This package contains a collection of 9 datasets, andrews and bakulski cord blood, blood gse35069, blood gse35069 chen, blood gse35069 complete, combined cord blood, cord bloo d gse68456, gervin and lyle cord blood, guintivano dlpfc and saliva gse48472. The data are used to estimate cell counts using Extrinsic epigenetic age acceleration (EEAA) method. It also contains a collection of 12 datasets to use with MethylClock package to estimate chronological and gestational DNA methylation with estimators to use with different methylation clocks.

r-affyio 1.80.0
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/bmbolstad/affyio
Licenses: LGPL 2.0+
Build system: r
Synopsis: Tools for parsing Affymetrix data files
Description:

This package provides routines for parsing Affymetrix data files based upon file format information. The primary focus is on accessing the CEL and CDF file formats.

r-bgmix 1.59.0
Propagated dependencies: r-kernsmooth@2.23-26
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BGmix/
Licenses: GPL 2
Build system: r
Synopsis: Bayesian models for differential gene expression
Description:

This package provides fully Bayesian mixture models for differential gene expression.

r-adacgh2 2.50.0
Dependencies: python-wrapper@3.11.14
Propagated dependencies: r-acgh@1.88.0 r-bit@4.6.0 r-cluster@2.1.8.1 r-dnacopy@1.84.0 r-ff@4.5.2 r-tilingarray@1.88.0 r-waveslim@1.8.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/rdiaz02/adacgh2
Licenses: GPL 3+
Build system: r
Synopsis: Big data analysis from aCGH experiments
Description:

This package analyzes and creates plots of array CGH data. Also, it allows usage of CBS, wavelet-based smoothing, HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.

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-organism-dplyr 1.37.1
Propagated dependencies: r-annotationdbi@1.72.0 r-annotationfilter@1.34.0 r-biocfilecache@3.0.0 r-dbi@1.2.3 r-dbplyr@2.5.1 r-dplyr@1.1.4 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rlang@1.1.6 r-rsqlite@2.4.4 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-tibble@3.3.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Organism.dplyr
Licenses: Artistic License 2.0
Build system: r
Synopsis: Dplyr-based access to Bioconductor annotation resources
Description:

This package provides an alternative interface to Bioconductor annotation resources, in particular the gene identifier mapping functionality of the org packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the TxDb packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

r-plyranges 1.30.1
Propagated dependencies: r-biocgenerics@0.56.0 r-dplyr@1.1.4 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-magrittr@2.0.4 r-rlang@1.1.6 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-tidyselect@1.2.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/plyranges
Licenses: Artistic License 2.0
Build system: r
Synopsis: Fluent interface for manipulating GenomicRanges
Description:

This package provides a dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessibility for new Bioconductor users is hopefully increased.

r-genomeinfodbdata 1.2.15
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GenomeInfoDbData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Species and taxonomy ID look up tables for GenomeInfoDb
Description:

This package contains data for mapping between NCBI taxonomy ID and species. It is used by functions in the GenomeInfoDb package.

r-scran 1.38.0
Propagated dependencies: r-beachmat@2.26.0 r-bh@1.87.0-1 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biocsingular@1.26.1 r-bluster@1.20.0 r-delayedarray@0.36.0 r-dqrng@0.4.1 r-edger@4.8.0 r-igraph@2.2.1 r-limma@3.66.0 r-matrix@1.7-4 r-matrixgenerics@1.22.0 r-metapod@1.18.0 r-rcpp@1.1.0 r-s4arrays@1.10.0 r-s4vectors@0.48.0 r-scuttle@1.20.0 r-singlecellexperiment@1.32.0 r-statmod@1.5.1 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/scran
Licenses: GPL 3
Build system: r
Synopsis: Methods for single-cell RNA-Seq data analysis
Description:

This package implements a variety of low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, and detection of highly variable and significantly correlated genes.

r-deseq 1.39.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-genefilter@1.92.0 r-geneplotter@1.88.0 r-lattice@0.22-7 r-locfit@1.5-9.12 r-mass@7.3-65 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www-huber.embl.de/users/anders/DESeq/
Licenses: GPL 3+
Build system: r
Synopsis: Differential gene expression analysis
Description:

This package provides tools for estimating variance-mean dependence in count data from high-throughput genetic sequencing assays and for testing for differential expression based on a model using the negative binomial distribution.

r-rtcgatoolbox 2.40.0
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-delayedarray@0.36.0 r-genomicranges@1.62.0 r-httr@1.4.7 r-raggedexperiment@1.34.0 r-rcurl@1.98-1.17 r-rjsonio@2.0.0 r-rvest@1.0.5 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-tcgautils@1.30.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://mksamur.github.io/RTCGAToolbox/
Licenses: GPL 2
Build system: r
Synopsis: Export TCGA Firehose data
Description:

Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. This package provides an extensible R based data client for Firehose pre-processed data.

r-biomformat 1.38.0
Propagated dependencies: r-jsonlite@2.0.0 r-matrix@1.7-4 r-plyr@1.8.9 r-rhdf5@2.54.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/joey711/biomformat/
Licenses: GPL 2
Build system: r
Synopsis: Interface package for the BIOM file format
Description:

This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the Python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.

r-illumina450probevariants-db 1.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Illumina450ProbeVariants.db
Licenses: GPL 3
Build system: r
Synopsis: Variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes
Description:

This package includes details on variants for each probe on the 450k bead chip for each of the four populations (Asian, American, African and European).

r-abn 3.1.12
Dependencies: gsl@2.8 jags@4.3.1
Propagated dependencies: r-doparallel@1.0.17 r-foreach@1.5.2 r-glmmtmb@1.1.13 r-graph@1.88.0 r-jsonlite@2.0.0 r-lme4@1.1-37 r-mclogit@0.9.6 r-nnet@7.3-20 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1 r-rgraphviz@2.54.0 r-rjags@4-17 r-stringi@1.8.7
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://r-bayesian-networks.org/
Licenses: GPL 2+
Build system: r
Synopsis: Modelling multivariate data with additive bayesian networks
Description:

Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a generalized linear model (GLM). Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. This package provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data.

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-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-msnid 1.44.0
Propagated dependencies: r-annotationdbi@1.72.0 r-annotationhub@4.0.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocstyle@2.38.0 r-biostrings@2.78.0 r-data-table@1.17.8 r-doparallel@1.0.17 r-dplyr@1.1.4 r-foreach@1.5.2 r-ggplot2@4.0.1 r-iterators@1.0.14 r-msmstests@1.48.0 r-msnbase@2.36.0 r-mzid@1.48.0 r-mzr@2.44.0 r-protgenerics@1.42.0 r-purrr@1.2.0 r-r-cache@0.17.0 r-rcpp@1.1.0 r-reshape2@1.4.5 r-rlang@1.1.6 r-runit@0.4.33.1 r-stringr@1.6.0 r-tibble@3.3.0 r-xtable@1.8-4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MSnID
Licenses: Artistic License 2.0
Build system: r
Synopsis: Utilities for LC-MSn proteomics identifications
Description:

This package extracts tandem mass spectrometry (MS/MS) ID data from mzIdentML (leveraging the mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. It also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.

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