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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-omnipathr 3.14.0
Propagated dependencies: r-checkmate@2.3.3 r-crayon@1.5.3 r-curl@7.0.0 r-digest@0.6.39 r-dplyr@1.1.4 r-httr@1.4.7 r-igraph@2.2.1 r-jsonlite@2.0.0 r-later@1.4.4 r-logger@0.4.1 r-lubridate@1.9.4 r-magrittr@2.0.4 r-progress@1.2.3 r-purrr@1.2.0 r-r-utils@2.13.0 r-rappdirs@0.3.3 r-readr@2.1.6 r-readxl@1.4.5 r-rlang@1.1.6 r-rmarkdown@2.30 r-rsqlite@2.4.4 r-rvest@1.0.5 r-stringi@1.8.7 r-stringr@1.6.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-tidyselect@1.2.1 r-vctrs@0.6.5 r-withr@3.0.2 r-xml@3.99-0.20 r-xml2@1.5.0 r-yaml@2.3.10 r-zip@2.3.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://saezlab.github.io/OmnipathR/
Licenses: Expat
Build system: r
Synopsis: OmniPath web service client and more
Description:

This package provides a client for the OmniPath web service and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data.

r-scdblfinder 1.24.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biocneighbors@2.4.0 r-biocparallel@1.44.0 r-biocsingular@1.26.1 r-bluster@1.20.0 r-delayedarray@0.36.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-igraph@2.2.1 r-iranges@2.44.0 r-mass@7.3-65 r-matrix@1.7-4 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-scater@1.38.0 r-scran@1.38.0 r-scuttle@1.20.0 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0 r-xgboost@1.7.11.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/plger/scDblFinder
Licenses: GPL 3
Build system: r
Synopsis: Detect multiplets in single-cell RNA sequencing data
Description:

The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell RNA sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly found in the scran package, and the new fast and comprehensive scDblFinder method.

r-icobra 1.38.0
Propagated dependencies: r-dplyr@1.1.4 r-dt@0.34.0 r-ggplot2@4.0.1 r-limma@3.66.0 r-reshape2@1.4.5 r-rlang@1.1.6 r-rocr@1.0-11 r-scales@1.4.0 r-shiny@1.11.1 r-shinybs@0.61.1 r-shinydashboard@0.7.3 r-upsetr@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/iCOBRA
Licenses: GPL 2+
Build system: r
Synopsis: Comparison and visualization of ranking and assignment methods
Description:

This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a Shiny application for interactive exploration of results.

r-bsgenome-hsapiens-ucsc-hg19 1.4.3
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Homo sapiens
Description:

This package provides full genome sequences for Homo sapiens as provided by UCSC (hg19, February 2009) and stored in Biostrings objects.

r-dittoseq 1.22.0
Propagated dependencies: r-colorspace@2.1-2 r-cowplot@1.2.0 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-ggridges@0.5.7 r-gridextra@2.3 r-pheatmap@1.0.13 r-reshape2@1.4.5 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/dittoSeq
Licenses: Expat
Build system: r
Synopsis: Single-cell and bulk RNA sequencing visualization
Description:

This package provides a universal, user friendly, single-cell and bulk RNA sequencing visualization toolkit that allows highly customizable creation of color blindness friendly, publication-quality figures. dittoSeq accepts both SingleCellExperiment (SCE) and Seurat objects, as well as the import and usage, via conversion to an SCE, of SummarizedExperiment or DGEList bulk data. Visualizations include dimensionality reduction plots, heatmaps, scatterplots, percent composition or expression across groups, and more. Customizations range from size and title adjustments to automatic generation of annotations for heatmaps, overlay of trajectory analysis onto any dimensionality reduciton plot, hidden data overlay upon cursor hovering via ggplotly conversion, and many more. All with simple, discrete inputs. Color blindness friendliness is powered by legend adjustments (enlarged keys), and by allowing the use of shapes or letter-overlay in addition to the carefully selected codedittoColors().

r-ensdb-mmusculus-v79 2.99.0
Propagated dependencies: r-ensembldb@2.34.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/EnsDb.Mmusculus.v79
Licenses: Artistic License 2.0
Build system: r
Synopsis: Ensembl based annotation package
Description:

This package exposes an annotation database generated from Ensembl.

r-gagedata 2.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/gageData
Licenses: GPL 2+
Build system: r
Synopsis: Auxiliary data for the gage package
Description:

This is a supportive data package for the software package gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included.

r-drimseq 1.38.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-edger@4.8.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-limma@3.66.0 r-mass@7.3-65 r-reshape2@1.4.5 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/DRIMSeq
Licenses: GPL 3+
Build system: r
Synopsis: Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
Description:

The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.

r-ucsc-utils 1.6.0
Propagated dependencies: r-httr@1.4.7 r-jsonlite@2.0.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/UCSC.utils
Licenses: Artistic License 2.0
Build system: r
Synopsis: Low-level utilities to retrieve data from the UCSC Genome Browser
Description:

This package provides a set of low-level utilities to retrieve data from the UCSC Genome Browser. Most functions in the package access the data via the UCSC REST API but some of them query the UCSC MySQL server directly. Note that the primary purpose of the package is to support higher-level functionalities implemented in downstream packages like GenomeInfoDb or txdbmaker.

r-decontam 1.30.0
Propagated dependencies: r-ggplot2@4.0.1 r-reshape2@1.4.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/benjjneb/decontam
Licenses: Artistic License 2.0
Build system: r
Synopsis: Identification of contaminants in marker-gene and metagenomics data
Description:

This package offers simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. It works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs, etc). Requires DNA quantitation data or sequenced negative control samples.

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-savr 1.37.0
Propagated dependencies: r-ggplot2@4.0.1 r-gridextra@2.3 r-reshape2@1.4.5 r-scales@1.4.0 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/bcalder/savR
Licenses: AGPL 3+
Build system: r
Synopsis: Parse and analyze Illumina SAV files
Description:

This package provides tools to parse Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots.

r-quantro 1.44.0
Propagated dependencies: r-biobase@2.70.0 r-doparallel@1.0.17 r-foreach@1.5.2 r-ggplot2@4.0.1 r-iterators@1.0.14 r-minfi@1.56.0 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/quantro/
Licenses: GPL 3+
Build system: r
Synopsis: Test for when to use quantile normalization
Description:

This package provides a data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.

r-asgsca 1.44.0
Propagated dependencies: r-mass@7.3-65 r-matrix@1.7-4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ASGSCA
Licenses: GPL 3
Build system: r
Synopsis: Analysis of associations between multiple genotypes and traits
Description:

The package ASGSCA (Association Study using Generalized Structured Component Analysis) provides tools to model and test the association between multiple genotypes and multiple traits, taking into account the prior biological knowledge. Genes, and clinical pathways are incorporated in the model as latent variables.

r-msnbase 2.36.0
Propagated dependencies: r-affy@1.88.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-digest@0.6.39 r-ggplot2@4.0.1 r-impute@1.84.0 r-iranges@2.44.0 r-lattice@0.22-7 r-maldiquant@1.22.3 r-mass@7.3-65 r-mscoreutils@1.21.0 r-mzid@1.48.0 r-mzr@2.44.0 r-pcamethods@2.2.0 r-plyr@1.8.9 r-protgenerics@1.42.0 r-psmatch@1.14.0 r-rcpp@1.1.0 r-s4vectors@0.48.0 r-scales@1.4.0 r-vsn@3.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/lgatto/MSnbase
Licenses: Artistic License 2.0
Build system: r
Synopsis: Base functions and classes for MS-based proteomics
Description:

This package provides basic plotting, data manipulation and processing of mass spectrometry based proteomics data.

r-adsplit 1.80.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biobase@2.70.0 r-cluster@2.1.8.1 r-go-db@3.22.0 r-keggrest@1.50.0 r-multtest@2.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://compdiag.molgen.mpg.de/software/adSplit.shtml
Licenses: GPL 2+
Build system: r
Synopsis: Annotation-driven splits in microarray data
Description:

This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.

r-annmap 1.52.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-dbi@1.2.3 r-digest@0.6.39 r-genefilter@1.92.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-lattice@0.22-7 r-rmysql@0.11.1 r-rsamtools@2.26.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/cruk-mi/annmap
Licenses: GPL 2
Build system: r
Synopsis: Genome annotation and visualisation for Affymetrix arrays and NGS analysis
Description:

This package annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided.

r-a4preproc 1.58.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/a4Preproc/
Licenses: GPL 3
Build system: r
Synopsis: Automated Affymetrix array analysis preprocessing package
Description:

This is a package for the automated analysis of Affymetrix arrays. It is used for preprocessing the arrays.

r-roar 1.46.0
Propagated dependencies: r-biocgenerics@0.56.0 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-iranges@2.44.0 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://github.com/vodkatad/roar/
Licenses: GPL 3
Build system: r
Synopsis: Identify differential APA usage from RNA-seq alignments
Description:

This package provides tools for identifying preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.

r-gcptools 1.0.0
Propagated dependencies: r-anvilbase@1.4.0 r-biocbaseutils@1.12.0 r-dplyr@1.1.4 r-httr@1.4.7 r-rlang@1.1.6 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/Bioconductor/GCPtools
Licenses: Artistic License 2.0
Build system: r
Synopsis: Tools for working with @code{gcloud} and @code{gsutil}
Description:

This package provides lower-level functionality to interface with Google Cloud Platform tools. gcloud and gsutil are both supported. The functionality provided centers around utilities for the AnVIL platform.

r-anota 1.58.0
Propagated dependencies: r-multtest@2.66.0 r-qvalue@2.42.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/anota/
Licenses: GPL 3
Build system: r
Synopsis: Analysis of translational activity
Description:

Genome wide studies of translational control is emerging as a tool to study various biological conditions. The output from such analysis is both the mRNA level (e.g. cytosolic mRNA level) and the level of mRNA actively involved in translation (the actively translating mRNA level) for each mRNA. The standard analysis of such data strives towards identifying differential translational between two or more sample classes - i.e., differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels. This package allows for such analysis using partial variances and the random variance model. As 10s of thousands of mRNAs are analyzed in parallel the library performs a number of tests to assure that the data set is suitable for such analysis.

r-genie3 1.32.0
Propagated dependencies: r-dplyr@1.1.4 r-reshape2@1.4.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GENIE3
Licenses: GPL 2+
Build system: r
Synopsis: Gene network inference with ensemble of trees
Description:

This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.

r-arraymvout 1.68.0
Propagated dependencies: r-affy@1.88.0 r-affycontam@1.68.0 r-biobase@2.70.0 r-lumi@2.62.0 r-mdqc@1.72.0 r-parody@1.68.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/arrayMvout
Licenses: Artistic License 2.0
Build system: r
Synopsis: Multivariate outlier detection for expression array QA
Description:

This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate.

r-gage 2.60.0
Propagated dependencies: r-annotationdbi@1.72.0 r-go-db@3.22.0 r-graph@1.88.0 r-keggrest@1.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-161
Licenses: GPL 2+
Build system: r
Synopsis: Generally applicable gene-set enrichment for pathway analysis
Description:

GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. The gage package provides functions for basic GAGE analysis, result processing and presentation. In addition, it provides demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These functions and data are also useful for gene set analysis using other methods.

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