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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.

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r-appreci8r 1.28.0
Propagated dependencies: r-xtrasnplocs-hsapiens-dbsnp144-grch37@0.99.12 r-variantannotation@1.56.0 r-txdb-hsapiens-ucsc-hg19-knowngene@3.22.1 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-snplocs-hsapiens-dbsnp144-grch37@0.99.20 r-sift-hsapiens-dbsnp137@1.0.0 r-shinyjs@2.1.0 r-shiny@1.11.1 r-seqinr@4.2-36 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-rentrez@1.2.4 r-polyphen-hsapiens-dbsnp131@1.0.2 r-openxlsx@4.2.8.1 r-mafdb-gnomadex-r2-1-hs37d5@3.10.0 r-mafdb-exac-r1-0-hs37d5@3.10.0 r-iranges@2.44.0 r-homo-sapiens@1.3.1 r-genomicscores@2.22.0 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-dt@0.34.0 r-cosmic-67@1.46.0 r-bsgenome-hsapiens-ucsc-hg19@1.4.3 r-bsgenome@1.78.0 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/appreci8R
Licenses: LGPL 3
Build system: r
Synopsis: appreci8R: an R/Bioconductor package for filtering SNVs and short indels with high sensitivity and high PPV
Description:

The appreci8R is an R version of our appreci8-algorithm - A Pipeline for PREcise variant Calling Integrating 8 tools. Variant calling results of our standard appreci8-tools (GATK, Platypus, VarScan, FreeBayes, LoFreq, SNVer, samtools and VarDict), as well as up to 5 additional tools is combined, evaluated and filtered.

r-affycompdata 1.48.0
Propagated dependencies: r-biobase@2.70.0 r-affycomp@1.86.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/affycompData
Licenses: GPL 2+
Build system: r
Synopsis: affycomp data
Description:

Data needed by the affycomp package.

r-anopheles-db0 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/anopheles.db0
Licenses: Artistic License 2.0
Build system: r
Synopsis: Base Level Annotation databases for anopheles
Description:

Base annotation databases for anopheles, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

r-assessorfdata 1.28.0
Propagated dependencies: r-rsqlite@2.4.4 r-decipher@3.6.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/AssessORFData
Licenses: GPL 3
Build system: r
Synopsis: Data and Files for the AssessORF Package
Description:

This package provides access to mapping and results objects generated by the AssessORF package, as well as the genome sequences for the strains corresponding to those objects.

r-allmll 1.50.0
Propagated dependencies: r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/ALLMLL
Licenses: GPL 2
Build system: r
Synopsis: subset of arrays from a large acute lymphoblastic leukemia (ALL) study
Description:

This package provides probe-level data for 20 HGU133A and 20 HGU133B arrays which are a subset of arrays from a large ALL study. The data is for the MLL arrays. This data was published in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 102: 2951-2959.

r-asurat 1.14.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-rcpp@1.1.0 r-plot3d@1.4.2 r-complexheatmap@2.26.0 r-cluster@2.1.8.1 r-circlize@0.4.16
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/ASURAT
Licenses: FSDG-compatible
Build system: r
Synopsis: Functional annotation-driven unsupervised clustering for single-cell data
Description:

ASURAT is a software for single-cell data analysis. Using ASURAT, one can simultaneously perform unsupervised clustering and biological interpretation in terms of cell type, disease, biological process, and signaling pathway activity. Inputting a single-cell RNA-seq data and knowledge-based databases, such as Cell Ontology, Gene Ontology, KEGG, etc., ASURAT transforms gene expression tables into original multivariate tables, termed sign-by-sample matrices (SSMs).

r-awaggregator 1.0.0
Propagated dependencies: r-toordinal@1.4-0.0 r-tidyr@1.3.1 r-stringr@1.6.0 r-rlang@1.1.6 r-ranger@0.17.0 r-purrr@1.2.0 r-progress@1.2.3 r-peptides@2.4.6 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://github.com/Tan-Jiahua/AWAggregator
Licenses: Expat
Build system: r
Synopsis: Attribute-Weighted Aggregation
Description:

This package implements an attribute-weighted aggregation algorithm which leverages peptide-spectrum match (PSM) attributes to provide a more accurate estimate of protein abundance compared to conventional aggregation methods. This algorithm employs pre-trained random forest models to predict the quantitative inaccuracy of PSMs based on their attributes. PSMs are then aggregated to the protein level using a weighted average, taking the predicted inaccuracy into account. Additionally, the package allows users to construct their own training sets that are more relevant to their specific experimental conditions if desired.

r-alabaster-sfe 1.2.0
Propagated dependencies: r-xml2@1.5.0 r-terra@1.8-86 r-summarizedexperiment@1.40.0 r-spdep@1.4-1 r-spatialreg@1.4-2 r-spatialfeatureexperiment@1.12.1 r-singlecellexperiment@1.32.0 r-sfarrow@0.4.1 r-s4vectors@0.48.0 r-rbioformats@1.10.0 r-jsonlite@2.0.0 r-ebimage@4.52.0 r-alabaster-spatial@1.10.0 r-alabaster-sce@1.10.0 r-alabaster-base@1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://pachterlab.github.io/alabaster.sfe/
Licenses: Expat
Build system: r
Synopsis: Language agnostic on disk serialization of SpatialFeatureExperiment
Description:

Builds upon the existing ArtifactDB project, expending alabaster.spatial for language agnostic on disk serialization of SpatialFeatureExperiment.

r-ahlrbasedbs 1.8.0
Propagated dependencies: r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/AHLRBaseDbs
Licenses: Artistic License 2.0
Build system: r
Synopsis: LRBaseDbs for AnnotationHub
Description:

Supplies AnnotationHub with `LRbaseDb` Ligand-Receptor annotation databases for many species. All the SQLite files are generated by our Snakemake workflow [lrbase-workflow](https://github.com/rikenbit/lrbase-workflow). For the details, see the README.md of lrbase-workflow.

r-artms 1.28.0
Propagated dependencies: r-yaml@2.3.10 r-venndiagram@1.7.3 r-upsetr@1.4.0 r-tidyr@1.3.1 r-stringr@1.6.0 r-seqinr@4.2-36 r-scales@1.4.0 r-rcolorbrewer@1.1-3 r-plyr@1.8.9 r-plotly@4.11.0 r-pheatmap@1.0.13 r-org-hs-eg-db@3.22.0 r-openxlsx@4.2.8.1 r-msstats@4.18.1 r-limma@3.66.0 r-gplots@3.2.0 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-ggdendro@0.2.0 r-getopt@1.20.4 r-dplyr@1.1.4 r-data-table@1.17.8 r-corrplot@0.95 r-cluster@2.1.8.1 r-circlize@0.4.16 r-bit64@4.6.0-1 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: http://artms.org
Licenses: FSDG-compatible
Build system: r
Synopsis: Analytical R tools for Mass Spectrometry
Description:

artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.

r-antiprofilesdata 1.46.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/antiProfilesData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Normal colon and cancer preprocessed affy data for antiProfile building
Description:

Colon normal tissue and cancer samples used in Corrada Bravo, et al. gene expression anti-profiles paper: BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. Measurements are z-scores obtained from the GeneExpression Barcode in the frma package.

r-alphamissenser 1.6.1
Propagated dependencies: r-whisker@0.4.1 r-spdl@0.0.5 r-rlang@1.1.6 r-rjsoncons@1.3.2 r-memoise@2.0.1 r-ggplot2@4.0.1 r-duckdb@1.4.2 r-dplyr@1.1.4 r-dbi@1.2.3 r-curl@7.0.0 r-biocfilecache@3.0.0 r-biocbaseutils@1.12.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://mtmorgan.github.io/AlphaMissenseR/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Accessing AlphaMissense Data Resources in R
Description:

The AlphaMissense publication <https://www.science.org/doi/epdf/10.1126/science.adg7492> outlines how a variant of AlphaFold / DeepMind was used to predict missense variant pathogenicity. Supporting data on Zenodo <https://zenodo.org/record/10813168> include, for instance, 71M variants across hg19 and hg38 genome builds. The AlphaMissenseR package allows ready access to the data, downloading individual files to DuckDB databases for exploration and integration into *R* and *Bioconductor* workflows.

r-alternativesplicingevents-hg38 1.1.0
Propagated dependencies: r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://github.com/nuno-agostinho/alternativeSplicingEvents.hg38
Licenses: Expat
Build system: r
Synopsis: Alternative splicing event annotation for Human (hg38)
Description:

Data frame containing alternative splicing events. The splicing events were compiled from the annotation files used by the alternative splicing quantification tools MISO, VAST-TOOLS, SUPPA and rMATS.

r-anvilpublish 1.20.0
Propagated dependencies: r-yaml@2.3.10 r-whisker@0.4.1 r-rmarkdown@2.30 r-readr@2.1.6 r-jsonlite@2.0.0 r-httr@1.4.7 r-biocmanager@1.30.27 r-biocbaseutils@1.12.0 r-anvilgcp@1.4.1 r-anvil@1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/AnVILPublish
Licenses: Artistic License 2.0
Build system: r
Synopsis: Publish Packages and Other Resources to AnVIL Workspaces
Description:

Use this package to create or update AnVIL workspaces from resources such as R / Bioconductor packages. The metadata about the package (e.g., select information from the package DESCRIPTION file and from vignette YAML headings) are used to populate the DASHBOARD'. Vignettes are translated to python notebooks ready for evaluation in AnVIL.

r-affyhgu133a2expr 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/Affyhgu133A2Expr
Licenses: FSDG-compatible
Build system: r
Synopsis: Affymetrix Human Genome U133A 2.0 Array (GPL571) Expression Data Package
Description:

This package contains pre-built human (GPL571) databases of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO.

r-ahcytobands 0.99.1
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/AHCytoBands
Licenses: Artistic License 2.0
Build system: r
Synopsis: CytoBands for AnnotationHub
Description:

Supplies AnnotationHub with CytoBand information from UCSC. There is a track for each major organism. Giemsa-stained bands are commonly used to decorate chromosomal overviews in visualizations of genomic data.

r-affymoe4302expr 1.48.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/Affymoe4302Expr
Licenses: FSDG-compatible
Build system: r
Synopsis: Affymetrix Mouse Genome 430 2.0 Array (GPL1261) Expression Data Package
Description:

This package contains pre-built mouse (GPL1261) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO.

r-arabidopsis-db0 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/arabidopsis.db0
Licenses: Artistic License 2.0
Build system: r
Synopsis: Base Level Annotation databases for arabidopsis
Description:

Base annotation databases for arabidopsis, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

r-anvilbilling 1.20.0
Propagated dependencies: r-shinytoastr@2.2.0 r-shiny@1.11.1 r-plotly@4.11.0 r-magrittr@2.0.4 r-lubridate@1.9.4 r-ggplot2@4.0.1 r-dt@0.34.0 r-dplyr@1.1.4 r-dbi@1.2.3 r-bigrquery@1.6.1
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/AnVILBilling
Licenses: Artistic License 2.0
Build system: r
Synopsis: Provide functions to retrieve and report on usage expenses in NHGRI AnVIL (anvilproject.org)
Description:

AnVILBilling helps monitor AnVIL-related costs in R, using queries to a BigQuery table to which costs are exported daily. Functions are defined to help categorize tasks and associated expenditures, and to visualize and explore expense profiles over time. This package will be expanded to help users estimate costs for specific task sets.

r-ahwikipathwaysdbs 0.99.4
Propagated dependencies: r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://github.com/kozo2/AHWikipathwaysDbs
Licenses: Artistic License 2.0
Build system: r
Synopsis: Metabolites linked to WikiPathways pathways (for AnnotationHub)
Description:

The package provides a comprehensive mapping table of metabolites linked to Wikipathways pathways. The tables include HMDB, KEGG, ChEBI, Drugbank, PubChem compound, ChemSpider, KNApSAcK, and Wikidata IDs plus CAS and InChIKey. The tables are provided for each of the 25 species ("Anopheles gambiae", "Arabidopsis thaliana", "Bacillus subtilis", "Bos taurus", "Caenorhabditis elegans", "Canis familiaris", "Danio rerio", "Drosophila melanogaster", "Equus caballus", "Escherichia coli", "Gallus gallus", "Gibberella zeae", "Homo sapiens", "Hordeum vulgare", "Mus musculus", "Mycobacterium tuberculosis", "Oryza sativa", "Pan troglodytes", "Plasmodium falciparum", "Populus trichocarpa", "Rattus norvegicus", "Saccharomyces cerevisiae", "Solanum lycopersicum", "Sus scrofa", "Zea mays"). These table information can be used for Metabolite Set Enrichment Analysis.

r-ath1121501frmavecs 1.0.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/ath1121501frmavecs
Licenses: GPL 2+
Build system: r
Synopsis: Vectors used by frma for microarrays of type ath1121501
Description:

Annotation package for the implementation of the frozen Robust Multiarray Analysis procedure for Arabidopsis thaliana. This package was generated on the basis of frmaTools version 1.52.0.

r-ag-db 3.13.0
Propagated dependencies: r-org-at-tair-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/ag.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix AG Array annotation data (chip ag)
Description:

Affymetrix Affymetrix AG Array annotation data (chip ag) assembled using data from public repositories.

r-ahpathbankdbs 0.99.5
Propagated dependencies: r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://github.com/kozo2/AHPathbankDbs
Licenses: Artistic License 2.0
Build system: r
Synopsis: Metabolites and proteins linked to PathBank pathways (for AnnotationHub)
Description:

The package provides a comprehensive mapping table of metabolites and proteins linked to PathBank pathways. The tables include HMDB, KEGG, ChEBI, CAS, Drugbank, Uniprot IDs. The tables are provided for each of the 10 species ("Homo sapiens", "Escherichia coli", "Mus musculus", "Arabidopsis thaliana", "Saccharomyces cerevisiae", "Bos taurus", "Caenorhabditis elegans", "Rattus norvegicus", "Drosophila melanogaster", and "Pseudomonas aeruginosa"). These table information can be used for Metabolite Set (and other) Enrichment Analysis.

r-adme16cod-db 3.4.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/adme16cod.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod)
Description:

Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod) assembled using data from public repositories.

Total results: 2909