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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-cogito 1.16.0
Propagated dependencies: r-txdb-mmusculus-ucsc-mm9-knowngene@3.2.2 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rmarkdown@2.30 r-magrittr@2.0.4 r-jsonlite@2.0.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-entropy@1.3.2 r-biocmanager@1.30.27 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/Cogito
Licenses: LGPL 3
Build system: r
Synopsis: Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets
Description:

Biological studies often consist of multiple conditions which are examined with different laboratory set ups like RNA-sequencing or ChIP-sequencing. To get an overview about the whole resulting data set, Cogito provides an automated, complete, reproducible and clear report about all samples and basic comparisons between all different samples. This report can be used as documentation about the data set or as starting point for further custom analysis.

r-clariomsmousetranscriptcluster-db 8.8.0
Propagated dependencies: r-org-mm-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/clariomsmousetranscriptcluster.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix clariomsmouse annotation data (chip clariomsmousetranscriptcluster)
Description:

Affymetrix clariomsmouse annotation data (chip clariomsmousetranscriptcluster) assembled using data from public repositories.

r-crisprbwa 1.14.0
Propagated dependencies: r-stringr@1.6.0 r-seqinfo@1.0.0 r-readr@2.1.6 r-rbwa@1.14.0 r-crisprbase@1.14.0 r-bsgenome@1.78.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/crisprVerse/crisprBwa
Licenses: Expat
Build system: r
Synopsis: BWA-based alignment of CRISPR gRNA spacer sequences
Description:

This package provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bwa. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Currently not supported on Windows machines.

r-cytofpower 1.16.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-shinymatrix@0.8.0 r-shinyjs@2.1.0 r-shinyfeedback@0.4.0 r-shiny@1.11.1 r-rlang@1.1.6 r-magrittr@2.0.4 r-ggplot2@4.0.1 r-dt@0.34.0 r-dplyr@1.1.4 r-diffcyt@1.30.0 r-cytoglmm@1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CyTOFpower
Licenses: LGPL 3
Build system: r
Synopsis: Power analysis for CyTOF experiments
Description:

This package is a tool to predict the power of CyTOF experiments in the context of differential state analyses. The package provides a shiny app with two options to predict the power of an experiment: i. generation of in-sicilico CyTOF data, using users input ii. browsing in a grid of parameters for which the power was already precomputed.

r-cernanetsim 1.22.0
Propagated dependencies: r-tidyr@1.3.1 r-tidygraph@1.3.1 r-tibble@3.3.0 r-rlang@1.1.6 r-purrr@1.2.0 r-igraph@2.2.1 r-ggraph@2.2.2 r-ggplot2@4.0.1 r-future@1.68.0 r-furrr@0.3.1 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/selcenari/ceRNAnetsim
Licenses: GPL 3+
Build system: r
Synopsis: Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)
Description:

This package simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one or more miRNA/mRNAs. The methodolgy adopted by the package has potential to incorparate any ceRNA (circRNA, lincRNA, etc.) into miRNA:target interaction network. The package basically distributes miRNA expression over available ceRNAs where each ceRNA attracks miRNAs proportional to its amount. But, the package can utilize multiple parameters that modify miRNA effect on its target (seed type, binding energy, binding location, etc.). The functions handle the given dataset as graph object and the processes progress via edge and node variables.

r-curatedadipoarray 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/MahShaaban/curatedAdipoArray
Licenses: FSDG-compatible
Build system: r
Synopsis: Curated Microarrays Dataset of MDI-induced Differentiated Adipocytes (3T3-L1) Under Genetic and Pharmacological Perturbations
Description:

This package provides a curated dataset of Microarrays samples. The samples are MDI- induced pre-adipocytes (3T3-L1) at different time points/stage of differentiation under different types of genetic (knockdown/overexpression) and pharmacological (drug treatment) perturbations. The package documents the data collection and processing. In addition to the documentation, the package contains the scripts that was used to generated the data.

r-crisprball 1.6.0
Propagated dependencies: r-shinywidgets@0.9.0 r-shinyjs@2.1.0 r-shinyjqui@0.4.1 r-shinycssloaders@1.1.0 r-shinybs@0.61.1 r-shiny@1.11.1 r-plotly@4.11.0 r-pcatools@2.20.0 r-matrixstats@1.5.0 r-interactivecomplexheatmap@1.18.1 r-htmlwidgets@1.6.4 r-ggplot2@4.0.1 r-dt@0.34.0 r-dittoseq@1.22.0 r-complexheatmap@2.26.0 r-colourpicker@1.3.0 r-circlize@0.4.16
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/j-andrews7/CRISPRball
Licenses: Expat
Build system: r
Synopsis: Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering
Description:

This package provides a Shiny application for visualization, exploration, comparison, and filtering of CRISPR screens analyzed with MAGeCK RRA or MLE. Features include interactive plots with on-click labeling, full customization of plot aesthetics, data upload and/or download, and much more. Quickly and easily explore your CRISPR screen results and generate publication-quality figures in seconds.

r-clariomdhumanprobeset-db 8.8.0
Propagated dependencies: r-org-hs-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/clariomdhumanprobeset.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix clariomdhuman annotation data (chip clariomdhumanprobeset)
Description:

Affymetrix clariomdhuman annotation data (chip clariomdhumanprobeset) assembled using data from public repositories.

r-celaref 1.28.0
Propagated dependencies: r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rlang@1.1.6 r-readr@2.1.6 r-matrix@1.7-4 r-mast@1.36.0 r-magrittr@2.0.4 r-ggplot2@4.0.1 r-dplyr@1.1.4 r-delayedarray@0.36.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/celaref
Licenses: GPL 3
Build system: r
Synopsis: Single-cell RNAseq cell cluster labelling by reference
Description:

After the clustering step of a single-cell RNAseq experiment, this package aims to suggest labels/cell types for the clusters, on the basis of similarity to a reference dataset. It requires a table of read counts per cell per gene, and a list of the cells belonging to each of the clusters, (for both test and reference data).

r-cytodx 1.30.0
Propagated dependencies: r-rpart-plot@3.1.4 r-rpart@4.1.24 r-glmnet@4.1-10 r-flowcore@2.22.0 r-dplyr@1.1.4 r-doparallel@1.0.17
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CytoDx
Licenses: GPL 2
Build system: r
Synopsis: Robust prediction of clinical outcomes using cytometry data without cell gating
Description:

This package provides functions that predict clinical outcomes using single cell data (such as flow cytometry data, RNA single cell sequencing data) without the requirement of cell gating or clustering.

r-camera 1.66.0
Propagated dependencies: r-xcms@4.8.0 r-rbgl@1.86.0 r-igraph@2.2.1 r-hmisc@5.2-4 r-graph@1.88.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: http://msbi.ipb-halle.de/msbi/CAMERA/
Licenses: GPL 2+
Build system: r
Synopsis: Collection of annotation related methods for mass spectrometry data
Description:

Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments.

r-consensusde 1.28.0
Propagated dependencies: r-txdb-dmelanogaster-ucsc-dm3-ensgene@3.2.2 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-ruvseq@1.44.0 r-rsamtools@2.26.0 r-rcolorbrewer@1.1-3 r-pcamethods@2.2.0 r-org-hs-eg-db@3.22.0 r-limma@3.66.0 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0 r-ensembldb@2.34.0 r-ensdb-hsapiens-v86@2.99.0 r-edger@4.8.0 r-edaseq@2.44.0 r-deseq2@1.50.2 r-dendextend@1.19.1 r-data-table@1.17.8 r-biostrings@2.78.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-biobase@2.70.0 r-annotationdbi@1.72.0 r-airway@1.30.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/consensusDE
Licenses: GPL 3
Build system: r
Synopsis: RNA-seq analysis using multiple algorithms
Description:

This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. Currently it supports "Voom", "EdgeR" and "DESeq". It uses RUV-seq (optional) to remove unwanted sources of variation.

r-curatedmetagenomicdata 3.18.0
Propagated dependencies: r-treesummarizedexperiment@2.18.0 r-tidyselect@1.2.1 r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-s4vectors@0.48.0 r-rlang@1.1.6 r-purrr@1.2.0 r-mia@1.18.0 r-magrittr@2.0.4 r-experimenthub@3.0.0 r-dplyr@1.1.4 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/waldronlab/curatedMetagenomicData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Curated Metagenomic Data of the Human Microbiome
Description:

The curatedMetagenomicData package provides standardized, curated human microbiome data for novel analyses. It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. The bacterial, fungal, and archaeal taxonomic abundances for each sample were calculated with MetaPhlAn3, and metabolic functional potential was calculated with HUMAnN3. The manually curated sample metadata and standardized metagenomic data are available as (Tree)SummarizedExperiment objects.

r-cager 2.16.0
Propagated dependencies: r-vgam@1.1-13 r-vegan@2.7-2 r-summarizedexperiment@1.40.0 r-stringi@1.8.7 r-stringdist@0.9.15 r-som@0.3-5.2 r-seqinfo@1.0.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rsamtools@2.26.0 r-rlang@1.1.6 r-reshape2@1.4.5 r-plyr@1.8.9 r-multiassayexperiment@1.36.1 r-memoise@2.0.1 r-matrix@1.7-4 r-kernsmooth@2.23-26 r-iranges@2.44.0 r-gtools@3.9.5 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0 r-formula-tools@1.7.1 r-data-table@1.17.8 r-cagefightr@1.30.0 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CAGEr
Licenses: GPL 3
Build system: r
Synopsis: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
Description:

The _CAGEr_ package identifies transcription start sites (TSS) and their usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across multiple CAGE experiments to construct consensus clusters (CC) representing the promoterome. CAGEr provides functions to profile expression levels of these clusters by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2 format for further facetting and customisation. After clustering, CAGEr performs analyses of promoter width and detects differential usage of TSSs (promoter shifting) between samples. CAGEr also exports its data as genome browser tracks, and as R objects for downsteam expression analysis by other Bioconductor packages such as DESeq2, CAGEfightR, or seqArchR.

r-cosiadata 1.10.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CoSIAdata
Licenses: Expat
Build system: r
Synopsis: VST normalized RNA-Sequencing data with annotations for multiple species samples from Bgee
Description:

Variance Stabilized Transformation of Read Counts derived from Bgee RNA-Seq Expression Data. Expression Data includes annotations and is across 6 species (Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Drosophila melanogaster, and Caenorhabditis elegans) and across more than 132 tissues. The data is represented as a RData files and is available in ExperimentHub.

r-circseqaligntk 1.12.0
Propagated dependencies: r-tidyr@1.3.1 r-shortread@1.68.0 r-shinyjs@2.1.0 r-shinyfiles@0.9.3 r-shiny@1.11.1 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-rlang@1.1.6 r-rhisat2@1.26.0 r-rbowtie2@2.16.0 r-r-utils@2.13.0 r-plotly@4.11.0 r-magrittr@2.0.4 r-iranges@2.44.0 r-htmltools@0.5.8.1 r-ggplot2@4.0.1 r-dplyr@1.1.4 r-biostrings@2.78.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/bitdessin/CircSeqAlignTk
Licenses: Expat
Build system: r
Synopsis: End-to-End Analysis of Small RNA-Seq Data from Viroids
Description:

CircSeqAlignTk is a toolkit for the analysis of RNA-Seq data derived from circular genome sequences, with a primary focus on viroids, circular RNAs typically consisting of a few hundred nucleotides. The toolkit supports an end-to-end analysis pipeline, from alignment to visualization.

r-clusterstab 1.82.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/clusterStab
Licenses: Artistic License 2.0
Build system: r
Synopsis: Compute cluster stability scores for microarray data
Description:

This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters.

r-cancerdata 1.48.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cancerdata
Licenses: GPL 2+
Build system: r
Synopsis: Development and validation of diagnostic tests from high-dimensional molecular data: Datasets
Description:

Dataset for the R package cancerclass.

r-crlmm 1.68.0
Propagated dependencies: r-vgam@1.1-13 r-rcppeigen@0.3.4.0.2 r-preprocesscore@1.72.0 r-oligoclasses@1.72.0 r-mvtnorm@1.3-3 r-matrixstats@1.5.0 r-limma@3.66.0 r-lattice@0.22-7 r-illuminaio@0.52.0 r-foreach@1.5.2 r-ff@4.5.2 r-ellipse@0.5.0 r-biocgenerics@0.56.0 r-biobase@2.70.0 r-beanplot@1.3.1 r-affyio@1.80.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/crlmm
Licenses: Artistic License 2.0
Build system: r
Synopsis: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays
Description:

Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms.

r-cottoncdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cottoncdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: cottoncdf
Description:

This package provides a package containing an environment representing the Cotton.cdf file.

r-crisprscore 1.14.0
Propagated dependencies: r-xvector@0.50.0 r-stringr@1.6.0 r-reticulate@1.44.1 r-randomforest@4.7-1.2 r-iranges@2.44.0 r-crisprscoredata@1.14.0 r-biostrings@2.78.0 r-biocgenerics@0.56.0 r-basilisk@1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/crisprVerse/crisprScore/issues
Licenses: Expat
Build system: r
Synopsis: On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs
Description:

This package provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target cutting efficiency scoring methods are RuleSet1, Azimuth, DeepHF, DeepCpf1, enPAM+GB, and CRISPRscan. Both the CFD and MIT scoring methods are available for off-target specificity prediction. The package also provides a Lindel-derived score to predict the probability of a gRNA to produce indels inducing a frameshift for the Cas9 nuclease. Note that DeepHF, DeepCpf1 and enPAM+GB are not available on Windows machines.

r-countsimqc 1.28.0
Propagated dependencies: r-tidyr@1.3.1 r-summarizedexperiment@1.40.0 r-rmarkdown@2.30 r-randtests@1.0.2 r-ragg@1.5.0 r-ggplot2@4.0.1 r-genomeinfodbdata@1.2.15 r-genefilter@1.92.0 r-edger@4.8.0 r-dt@0.34.0 r-dplyr@1.1.4 r-deseq2@1.50.2 r-catools@1.18.3
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/csoneson/countsimQC
Licenses: FSDG-compatible
Build system: r
Synopsis: Compare Characteristic Features of Count Data Sets
Description:

countsimQC provides functionality to create a comprehensive report comparing a broad range of characteristics across a collection of count matrices. One important use case is the comparison of one or more synthetic count matrices to a real count matrix, possibly the one underlying the simulations. However, any collection of count matrices can be compared.

r-csar 1.62.0
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-iranges@2.44.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CSAR
Licenses: Artistic License 2.0
Build system: r
Synopsis: Statistical tools for the analysis of ChIP-seq data
Description:

Statistical tools for ChIP-seq data analysis. The package includes the statistical method described in Kaufmann et al. (2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation.

r-cemitool 1.34.0
Propagated dependencies: r-wgcna@1.73 r-stringr@1.6.0 r-sna@2.8 r-scales@1.4.0 r-rmarkdown@2.30 r-pracma@2.4.6 r-network@1.19.0 r-matrixstats@1.5.0 r-knitr@1.50 r-intergraph@2.0-4 r-igraph@2.2.1 r-htmltools@0.5.8.1 r-gtable@0.3.6 r-gridextra@2.3 r-ggthemes@5.1.0 r-ggrepel@0.9.6 r-ggpmisc@0.6.2 r-ggplot2@4.0.1 r-ggdendro@0.2.0 r-fgsea@1.36.0 r-fastcluster@1.3.0 r-dt@0.34.0 r-dplyr@1.1.4 r-data-table@1.17.8 r-clusterprofiler@4.18.2
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CEMiTool
Licenses: GPL 3
Build system: r
Synopsis: Co-expression Modules identification Tool
Description:

The CEMiTool package unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.

Total results: 2909