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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-ccpromise 1.36.0
Propagated dependencies: r-promise@1.62.0 r-gseabase@1.72.0 r-ccp@1.2 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CCPROMISE
Licenses: GPL 2+
Build system: r
Synopsis: PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data
Description:

Perform Canonical correlation between two forms of high demensional genetic data, and associate the first compoent of each form of data with a specific biologically interesting pattern of associations with multiple endpoints. A probe level analysis is also implemented.

r-crisprshiny 1.6.0
Propagated dependencies: r-waiter@0.2.5-1.927501b r-shinyjs@2.1.0 r-shinybs@0.61.1 r-shiny@1.11.1 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-pwalign@1.6.0 r-htmlwidgets@1.6.4 r-dt@0.34.0 r-crisprviz@1.12.0 r-crisprscore@1.14.0 r-crisprdesign@1.12.0 r-crisprbase@1.14.0 r-bsgenome@1.78.0 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/crisprVerse/crisprShiny
Licenses: Expat
Build system: r
Synopsis: Exploring curated CRISPR gRNAs via Shiny
Description:

This package provides means to interactively visualize guide RNAs (gRNAs) in GuideSet objects via Shiny application. This GUI can be self-contained or as a module within a larger Shiny app. The content of the app reflects the annotations present in the passed GuideSet object, and includes intuitive tools to examine, filter, and export gRNAs, thereby making gRNA design more user-friendly.

r-cadd-v1-6-hg38 3.18.1
Propagated dependencies: r-genomicscores@2.22.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cadd.v1.6.hg38
Licenses: Artistic License 2.0
Build system: r
Synopsis: CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg38
Description:

Store University of Washington CADD v1.6 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.

r-chromatograms 1.0.0
Propagated dependencies: r-spectra@1.20.0 r-s4vectors@0.48.0 r-protgenerics@1.42.0 r-mscoreutils@1.21.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/RforMassSpectrometry/Chromatograms
Licenses: Artistic License 2.0
Build system: r
Synopsis: Infrastructure for Chromatographic Mass Spectrometry Data
Description:

The Chromatograms packages defines an efficient infrastructure for storing and handling of chromatographic mass spectrometry data. It provides different implementations of *backends* to store and represent the data. Such backends can be optimized for small memory footprint or fast data access/processing. A lazy evaluation queue and chunk-wise processing capabilities ensure efficient analysis of also very large data sets.

r-concordexr 1.10.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-spatialexperiment@1.20.0 r-sparsematrixstats@1.22.0 r-singlecellexperiment@1.32.0 r-rlang@1.1.6 r-purrr@1.2.0 r-matrix@1.7-4 r-delayedarray@0.36.0 r-cli@3.6.5 r-bluster@1.20.0 r-biocparallel@1.44.0 r-biocneighbors@2.4.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/pachterlab/concordexR
Licenses: Artistic License 2.0
Build system: r
Synopsis: Identify Spatial Homogeneous Regions with concordex
Description:

Spatial homogeneous regions (SHRs) in tissues are domains that are homogenous with respect to cell type composition. We present a method for identifying SHRs using spatial transcriptomics data, and demonstrate that it is efficient and effective at finding SHRs for a wide variety of tissue types. concordex relies on analysis of k-nearest-neighbor (kNN) graphs. The tool is also useful for analysis of non-spatial transcriptomics data, and can elucidate the extent of concordance between partitions of cells derived from clustering algorithms, and transcriptomic similarity as represented in kNN graphs.

r-cancer 1.44.0
Propagated dependencies: r-tkrplot@0.0-30 r-tidyr@1.3.1 r-survival@3.8-3 r-runit@0.4.33.1 r-rpart@4.1.24 r-r-oo@1.27.1 r-r-methodss3@1.8.2 r-plyr@1.8.9 r-phenotest@1.58.0 r-gseabase@1.72.0 r-genetclassifier@1.50.0 r-formula@1.2-5 r-dplyr@1.1.4 r-circlize@0.4.16 r-cbioportaldata@2.22.1 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/canceR
Licenses: GPL 2
Build system: r
Synopsis: Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC
Description:

The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

r-crcl18 1.30.0
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/CRCL18
Licenses: GPL 2
Build system: r
Synopsis: CRC cell line dataset
Description:

colorectal cancer mRNA and miRNA on 18 cell lines.

r-ccdata 1.36.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/ccdata
Licenses: Expat
Build system: r
Synopsis: Data for Combination Connectivity Mapping (ccmap) Package
Description:

This package contains microarray gene expression data generated from the Connectivity Map build 02 and LINCS l1000. The data are used by the ccmap package to find drugs and drug combinations to mimic or reverse a gene expression signature.

r-consensusov 1.32.0
Propagated dependencies: r-randomforest@4.7-1.2 r-matrixstats@1.5.0 r-limma@3.66.0 r-gsva@2.4.1 r-genefu@2.42.0 r-gdata@3.0.1 r-biocparallel@1.44.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: http://www.pmgenomics.ca/bhklab/software/consensusOV
Licenses: Artistic License 2.0
Build system: r
Synopsis: Gene expression-based subtype classification for high-grade serous ovarian cancer
Description:

This package implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer as described by Helland et al. (PLoS One, 2011), Bentink et al. (PLoS One, 2012), Verhaak et al. (J Clin Invest, 2013), and Konecny et al. (J Natl Cancer Inst, 2014). In addition, the package implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of clearly defined subtype.

r-chromscape 1.20.0
Propagated dependencies: r-viridis@0.6.5 r-umap@0.2.10.0 r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-stringdist@0.9.15 r-singlecellexperiment@1.32.0 r-shinywidgets@0.9.0 r-shinyjs@2.1.0 r-shinyhelper@0.3.2 r-shinyfiles@0.9.3 r-shinydashboardplus@2.0.6 r-shinydashboard@0.7.3 r-shinycssloaders@1.1.0 r-shiny@1.11.1 r-scran@1.38.0 r-scater@1.38.0 r-s4vectors@0.48.0 r-rtsne@0.17 r-rtracklayer@1.70.0 r-rsamtools@2.26.0 r-rlist@0.4.6.2 r-rcpp@1.1.0 r-qualv@0.3-5 r-qs@0.27.3 r-plotly@4.11.0 r-msigdbr@25.1.1 r-matrixtests@0.2.3.1 r-matrix@1.7-4 r-kableextra@1.4.0 r-jsonlite@2.0.0 r-irlba@2.3.5.1 r-iranges@2.44.0 r-gridextra@2.3 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-gggenes@0.5.1 r-genomicranges@1.62.0 r-fs@1.6.6 r-forcats@1.0.1 r-edger@4.8.0 r-dt@0.34.0 r-dplyr@1.1.4 r-delayedarray@0.36.0 r-coop@0.6-3 r-consensusclusterplus@1.74.0 r-colourpicker@1.3.0 r-colorramps@2.3.4 r-biocparallel@1.44.0 r-batchelor@1.26.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/vallotlab/ChromSCape
Licenses: GPL 3
Build system: r
Synopsis: Analysis of single-cell epigenomics datasets with a Shiny App
Description:

ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.

r-cfassay 1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CFAssay
Licenses: LGPL 2.0+
Build system: r
Synopsis: Statistical analysis for the Colony Formation Assay
Description:

The package provides functions for calculation of linear-quadratic cell survival curves and for ANOVA of experimental 2-way designs along with the colony formation assay.

r-cbpmanager 1.18.0
Propagated dependencies: r-vroom@1.6.6 r-shinydashboard@0.7.3 r-shinycssloaders@1.1.0 r-shinybs@0.61.1 r-shiny@1.11.1 r-rlang@1.1.6 r-rintrojs@0.3.4 r-reticulate@1.44.1 r-rapportools@1.2 r-plyr@1.8.9 r-markdown@2.0 r-magrittr@2.0.4 r-jsonlite@2.0.0 r-htmltools@0.5.8.1 r-dt@0.34.0 r-dplyr@1.1.4 r-basilisk@1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://arsenij-ust.github.io/cbpManager/index.html
Licenses: FSDG-compatible
Build system: r
Synopsis: Generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics
Description:

This R package provides an R Shiny application that enables the user to generate, manage, and edit data and metadata files suitable for the import in cBioPortal for Cancer Genomics. Create cancer studies and edit its metadata. Upload mutation data of a patient that will be concatenated to the data_mutation_extended.txt file of the study. Create and edit clinical patient data, sample data, and timeline data. Create custom timeline tracks for patients.

r-chevreulshiny 1.2.0
Propagated dependencies: r-wiggleplotr@1.34.0 r-waiter@0.2.5-1.927501b r-tidyselect@1.2.1 r-tidyr@1.3.1 r-tibble@3.3.0 r-stringr@1.6.0 r-singlecellexperiment@1.32.0 r-shinywidgets@0.9.0 r-shinyjs@2.1.0 r-shinyhelper@0.3.2 r-shinyfiles@0.9.3 r-shinydashboard@0.7.3 r-shiny@1.11.1 r-scales@1.4.0 r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-readr@2.1.6 r-rappdirs@0.3.3 r-purrr@1.2.0 r-plotly@4.11.0 r-patchwork@1.3.2 r-ggplotify@0.1.3 r-ggplot2@4.0.1 r-future@1.68.0 r-fs@1.6.6 r-enhancedvolcano@1.26.0 r-dt@0.34.0 r-dplyr@1.1.4 r-dbi@1.2.3 r-dataeditr@0.1.5 r-complexheatmap@2.26.0 r-clustree@0.5.1 r-chevreulprocess@1.2.0 r-chevreulplot@1.2.0 r-alabaster-base@1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/whtns/chevreulShiny
Licenses: Expat
Build system: r
Synopsis: Tools for managing SingleCellExperiment objects as projects
Description:

This package provides tools for managing SingleCellExperiment objects as projects. Includes functions for analysis and visualization of single-cell data. Also included is a shiny app for visualization of pre-processed scRNA data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

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-cosnet 1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/m1frasca/COSNet_GitHub
Licenses: GPL 2+
Build system: r
Synopsis: Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings
Description:

Package that implements the COSNet classification algorithm. The algorithm predicts node labels in partially labeled graphs where few positives are available for the class being predicted.

r-covrna 1.36.0
Propagated dependencies: r-genefilter@1.92.0 r-biobase@2.70.0 r-ade4@1.7-23
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/covRNA
Licenses: GPL 2+
Build system: r
Synopsis: Multivariate Analysis of Transcriptomic Data
Description:

This package provides the analysis methods fourthcorner and RLQ analysis for large-scale transcriptomic data.

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-copa 1.78.0
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/copa
Licenses: Artistic License 2.0
Build system: r
Synopsis: Functions to perform cancer outlier profile analysis
Description:

COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles.

r-citefuse 1.22.0
Propagated dependencies: r-uwot@0.2.4 r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-scran@1.38.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rtsne@0.17 r-rlang@1.1.6 r-rhdf5@2.54.0 r-reshape2@1.4.5 r-rcpp@1.1.0 r-randomforest@4.7-1.2 r-pheatmap@1.0.13 r-mixtools@2.0.0.1 r-matrix@1.7-4 r-igraph@2.2.1 r-gridextra@2.3 r-ggridges@0.5.7 r-ggraph@2.2.2 r-ggplot2@4.0.1 r-dbscan@1.2.3 r-cowplot@1.2.0 r-compositions@2.0-9
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CiteFuse
Licenses: GPL 3
Build system: r
Synopsis: CiteFuse: multi-modal analysis of CITE-seq data
Description:

CiteFuse pacakage implements a suite of methods and tools for CITE-seq data from pre-processing to integrative analytics, including doublet detection, network-based modality integration, cell type clustering, differential RNA and protein expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualisation of the analyses.

r-cycle 1.64.0
Propagated dependencies: r-mfuzz@2.70.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: http://cycle.sysbiolab.eu
Licenses: GPL 2
Build system: r
Synopsis: Significance of periodic expression pattern in time-series data
Description:

Package for assessing the statistical significance of periodic expression based on Fourier analysis and comparison with data generated by different background models.

r-copdsexualdimorphism-data 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/COPDSexualDimorphism.data
Licenses: LGPL 2.1
Build system: r
Synopsis: Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation
Description:

Datasets to support COPDSexaulDimorphism Package.

r-cellmapperdata 1.36.0
Propagated dependencies: r-experimenthub@3.0.0 r-cellmapper@1.36.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CellMapperData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Pre-processed data for use with the CellMapper package
Description:

Experiment data package. Contains microarray data from several large expression compendia that have been pre-processed for use with the CellMapper package. This pre-processed data is recommended for routine searches using the CellMapper package.

r-cnvranger 1.26.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-snprelate@1.44.0 r-s4vectors@0.48.0 r-reshape2@1.4.5 r-rappdirs@0.3.3 r-raggedexperiment@1.34.0 r-qqman@0.1.9 r-plyr@1.8.9 r-limma@3.66.0 r-lattice@0.22-7 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-gdsfmt@1.46.0 r-gdsarray@1.30.0 r-edger@4.8.0 r-data-table@1.17.8 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/CNVRanger
Licenses: Artistic License 2.0
Build system: r
Synopsis: Summarization and expression/phenotype association of CNV ranges
Description:

The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes.

r-cnorode 1.52.0
Propagated dependencies: r-genalg@0.2.1 r-cellnoptr@1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CNORode
Licenses: GPL 2
Build system: r
Synopsis: ODE add-on to CellNOptR
Description:

Logic based ordinary differential equation (ODE) add-on to CellNOptR.

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