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/_/ /      / / /____\/ /       \ \_\\ \/___/ /
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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-genomationdata 1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioinformatics.mdc-berlin.de/genomation/
Licenses: GPL 3+
Synopsis: Experimental data for use with the genomation package
Description:

This package contains experimental genetic data for use with the genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.

r-biobtreer 1.20.0
Propagated dependencies: r-httpuv@1.6.16 r-httr@1.4.7 r-jsonlite@2.0.0 r-stringi@1.8.7
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/tamerh/biobtreeR
Licenses: Expat
Synopsis: Use biobtree tool from R
Description:

The biobtreeR package provides an interface to biobtree, a tool which covers large sets of bioinformatics datasets and allows search and chain mappings functionalities.

r-cardelino 1.10.0
Propagated dependencies: r-combinat@0.0-8 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-ggtree@3.16.0 r-matrix@1.7-3 r-matrixstats@1.5.0 r-pheatmap@1.0.12 r-s4vectors@0.46.0 r-snpstats@1.58.0 r-variantannotation@1.54.1 r-vcfr@1.15.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/single-cell-genetics/cardelino
Licenses: GPL 3
Synopsis: Clone identification from single cell data
Description:

This package provides methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used.

r-inspect 1.38.0
Propagated dependencies: r-biobase@2.68.0 r-biocgenerics@0.54.0 r-biocparallel@1.42.0 r-deseq2@1.48.1 r-desolve@1.40 r-genomeinfodb@1.44.0 r-genomicalignments@1.44.0 r-genomicfeatures@1.60.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-kernsmooth@2.23-26 r-plgem@1.80.0 r-proc@1.18.5 r-readxl@1.4.5 r-rootsolve@1.8.2.4 r-rsamtools@2.24.0 r-rtracklayer@1.68.0 r-s4vectors@0.46.0 r-shiny@1.10.0 r-summarizedexperiment@1.38.1 r-txdb-mmusculus-ucsc-mm9-knowngene@3.2.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/INSPEcT
Licenses: GPL 2
Synopsis: Analysis of 4sU-seq and RNA-seq time-course data
Description:

INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and assess via modeling the rates that determines changes in mature mRNA levels.

r-hpo-db 0.99.2
Propagated dependencies: r-annotationdbi@1.70.0 r-annotationhub@3.16.0 r-biocfilecache@2.16.0 r-dbi@1.2.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/HPO.db
Licenses: Artistic License 2.0
Synopsis: Annotation maps describing the entire Human Phenotype Ontology
Description:

Human Phenotype Ontology (HPO) was developed to create a consistent description of gene products with disease perspectives, and is essential for supporting functional genomics in disease context. Accurate disease descriptions can discover new relationships between genes and disease, and new functions for previous uncharacteried genes and alleles.

r-zfpkm 1.30.0
Propagated dependencies: r-checkmate@2.3.2 r-dplyr@1.1.4 r-ggplot2@3.5.2 r-summarizedexperiment@1.38.1 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
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-alphabeta 1.22.0
Propagated dependencies: r-biocparallel@1.42.0 r-data-table@1.17.4 r-dplyr@1.1.4 r-expm@1.0-0 r-ggplot2@3.5.2 r-gtools@3.9.5 r-igraph@2.1.4 r-optimx@2025-4.9 r-plotly@4.10.4 r-stringr@1.5.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AlphaBeta
Licenses: GPL 3
Synopsis: Estimate epimutation rates and spectra from DNA methylations in plants
Description:

The package AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants. The method has been specifically designed to:

  • analyze germline epimutations in the context of multi-generational mutation accumulation lines;

  • analyze somatic epimutations in the context of plant development and aging.

r-txdb-mmusculus-ucsc-mm10-knowngene 3.10.0
Propagated dependencies: r-annotationdbi@1.70.0 r-genomicfeatures@1.60.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/
Licenses: Artistic License 2.0
Synopsis: Annotation package for TxDb knownGene object(s) for Mouse
Description:

This package loads a TxDb object, which is an R interface to prefabricated databases contained in this package. This package provides the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) based on the knownGene track.

r-decipher 3.4.0
Propagated dependencies: r-biostrings@2.76.0 r-dbi@1.2.3 r-iranges@2.42.0 r-s4vectors@0.46.0 r-xvector@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/DECIPHER/
Licenses: GPL 3
Synopsis: Tools for deciphering and managing biological sequences
Description:

This package provides a toolset for deciphering and managing biological sequences.

r-cpp11bigwig 0.1.1
Dependencies: curl@8.6.0 zlib@1.3.1
Propagated dependencies: r-cpp11@0.5.2 r-genomicranges@1.60.0 r-iranges@2.42.0 r-tibble@3.2.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://rnabioco.github.io/cpp11bigwig/
Licenses: Expat
Synopsis: Read bigWig and bigBed files
Description:

Read bigWig and bigBed files using libBigWig. This package provides lightweight access to the binary bigWig and bigBed formats developed by the UCSC Genome Browser group.

r-gypsum 1.4.0
Propagated dependencies: r-filelock@1.0.3 r-httr2@1.1.2 r-jsonlite@2.0.0 r-rappdirs@0.3.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ArtifactDB/gypsum-R
Licenses: Expat
Synopsis: Interface to the gypsum REST API
Description:

This package provides a client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various administrative and management tasks. Check out the documentation at https://github.com/ArtifactDB/gypsum-worker for more details.

r-trajectoryutils 1.16.1
Propagated dependencies: r-igraph@2.1.4 r-matrix@1.7-3 r-s4vectors@0.46.0 r-singlecellexperiment@1.30.1 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/TrajectoryUtils
Licenses: GPL 3
Synopsis: Single-cell trajectory analysis utilities
Description:

This package implements low-level utilities for single-cell trajectory analysis, primarily intended for re-use inside higher-level packages. It includes a function to create a cluster-level minimum spanning tree and data structures to hold pseudotime inference results.

r-dirichletmultinomial 1.50.0
Dependencies: gsl@2.8
Propagated dependencies: r-biocgenerics@0.54.0 r-iranges@2.42.0 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/DirichletMultinomial
Licenses: LGPL 3
Synopsis: Dirichlet-Multinomial mixture models for microbiome data
Description:

Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15.

r-agimicrorna 2.58.0
Propagated dependencies: r-affy@1.86.0 r-affycoretools@1.80.0 r-biobase@2.68.0 r-limma@3.64.1 r-preprocesscore@1.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://git.bioconductor.org/packages/AgiMicroRna
Licenses: GPL 3
Synopsis: Processing and differential expression analysis of Agilent microRNA chips
Description:

AgiMicroRna provides useful functionality for the processing, quality assessment and differential expression analysis of Agilent microRNA array data. The package uses a limma-like structure to generate the processed data in order to make statistical inferences about differential expression using the linear model features implemented in limma. Standard Bioconductor objects are used so that other packages could be used as well.

r-mutoss 0.1-13
Propagated dependencies: r-multcomp@1.4-28 r-multtest@2.64.0 r-mvtnorm@1.3-3 r-plotrix@3.8-4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/kornl/mutoss/
Licenses: GPL 2+ GPL 3+
Synopsis: Unified multiple testing procedures
Description:

This package is designed to ease the application and comparison of multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods are standardized and usable by the accompanying mutossGUI package.

r-biocstyle 2.36.0
Propagated dependencies: r-biocmanager@1.30.25 r-bookdown@0.43 r-knitr@1.50 r-rmarkdown@2.29 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
Synopsis: Bioconductor formatting styles
Description:

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

r-chipexoqualexample 1.32.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.github.com/keleslab/ChIPexoQualExample
Licenses: GPL 2+
Synopsis: Example data for the ChIPexoQual package
Description:

This package contains data for the ChIPexoQual package, consisting of 3 chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome.

r-hahmmr 1.0.0
Propagated dependencies: r-data-table@1.17.4 r-dplyr@1.1.4 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-glue@1.8.0 r-iranges@2.42.0 r-patchwork@1.3.0 r-rcpp@1.0.14 r-rcpparmadillo@14.4.3-1 r-roptim@0.1.6 r-stringr@1.5.1 r-tibble@3.2.1 r-zoo@1.8-14
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/package=hahmmr
Licenses: Expat
Synopsis: Haplotype-aware Hidden Markov Model for RNA
Description:

Haplotype-aware Hidden Markov Model for RNA (HaHMMR) is a method for detecting copy number variations (CNVs) from bulk RNA-seq data. Additional examples, documentations, and details on the method are available at https://github.com/kharchenkolab/hahmmr/.

r-xcir 1.8.0-1.3b59d45
Propagated dependencies: r-biomart@2.64.0 r-biostrings@2.76.0 r-data-table@1.17.4 r-ggplot2@3.5.2 r-iranges@2.42.0 r-readxl@1.4.5 r-s4vectors@0.46.0 r-seqminer@9.7 r-variantannotation@1.54.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/SRenan/XCIR
Licenses: GPL 2
Synopsis: Analysis of X chromosome inactivation
Description:

This package is an R package that offers models and tools for subject level analysis of X chromosome inactivation (XCI) and XCI-escape inference.

r-bsgenome-hsapiens-ncbi-grch38 1.3.1000
Propagated dependencies: r-bsgenome@1.76.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/release/data/annotation/html/BSgenome.Hsapiens.NCBI.GRCh38.html
Licenses: Artistic License 2.0
Synopsis: Full genome sequences for Homo sapiens (GRCh38)
Description:

This package provides full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.

r-polyphen-hsapiens-dbsnp131 1.0.2
Propagated dependencies: r-annotationdbi@1.70.0 r-rsqlite@2.3.11 r-variantannotation@1.54.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/PolyPhen.Hsapiens.dbSNP131
Licenses: Artistic License 2.0
Synopsis: PolyPhen predictions for Homo sapiens dbSNP build 131
Description:

This package provides a database of PolyPhen predictions for Homo sapiens dbSNP build 131.

r-bader 1.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BADER
Licenses: GPL 2
Synopsis: Bayesian analysis of differential expression in RNA sequencing data
Description:

The BADER package is intended for the analysis of RNA sequencing data. The algorithm fits a Bayesian hierarchical model for RNA sequencing count data. BADER returns the posterior probability of differential expression for each gene between two groups A and B. The joint posterior distribution of the variables in the model can be returned in the form of posterior samples, which can be used for further down-stream analyses such as gene set enrichment.

r-asics 2.24.0
Propagated dependencies: r-biocparallel@1.42.0 r-ggplot2@3.5.2 r-glmnet@4.1-8 r-gridextra@2.3 r-matrix@1.7-3 r-mvtnorm@1.3-3 r-pepsnmr@1.26.0 r-plyr@1.8.9 r-quadprog@1.5-8 r-ropls@1.40.0 r-summarizedexperiment@1.38.1 r-zoo@1.8-14
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ASICS
Licenses: GPL 2+
Synopsis: Automatic statistical identification in complex spectra
Description:

ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty.

r-beadarray 2.58.0
Propagated dependencies: r-annotationdbi@1.70.0 r-beaddatapackr@1.60.0 r-biobase@2.68.0 r-biocgenerics@0.54.0 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-hexbin@1.28.5 r-illuminaio@0.50.0 r-iranges@2.42.0 r-limma@3.64.1 r-reshape2@1.4.4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/beadarray
Licenses: Expat
Synopsis: Quality assessment and low-level analysis for Illumina BeadArray data
Description:

The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.

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Total results: 45109