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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-cntools 1.66.0
Propagated dependencies: r-genefilter@1.92.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CNTools
Licenses: LGPL 2.0+
Build system: r
Synopsis: Convert segment data into a region by sample matrix to allow for other high level computational analyses
Description:

This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data.

r-crisprdesign 1.12.0
Propagated dependencies: r-variantannotation@1.56.0 r-txdbmaker@1.6.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-matrixgenerics@1.22.0 r-matrix@1.7-4 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomeinfodb@1.46.0 r-crisprscore@1.14.0 r-crisprbowtie@1.14.0 r-crisprbase@1.14.0 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocgenerics@0.56.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/crisprVerse/crisprDesign
Licenses: Expat
Build system: r
Synopsis: Comprehensive design of CRISPR gRNAs for nucleases and base editors
Description:

This package provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.

r-cmap 1.15.1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cMAP
Licenses: LGPL 2.0+
Build system: r
Synopsis: data package containing annotation data for cMAP
Description:

Annotation data file for cMAP assembled using data from public data repositories.

r-cmapr 1.22.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-rhdf5@2.54.0 r-matrixstats@1.5.0 r-flowcore@2.22.0 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/cmap/cmapR
Licenses: FSDG-compatible
Build system: r
Synopsis: CMap Tools in R
Description:

The Connectivity Map (CMap) is a massive resource of perturbational gene expression profiles built by researchers at the Broad Institute and funded by the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) program. Please visit https://clue.io for more information. The cmapR package implements methods to parse, manipulate, and write common CMap data objects, such as annotated matrices and collections of gene sets.

r-cellbarcode 1.16.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-stringr@1.6.0 r-shortread@1.68.0 r-seqinr@4.2-36 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-rcpp@1.1.0 r-plyr@1.8.9 r-magrittr@2.0.4 r-ggplot2@4.0.1 r-egg@0.4.5 r-data-table@1.17.8 r-ckmeans-1d-dp@4.3.5 r-biostrings@2.78.0 r-bh@1.87.0-1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://wenjie1991.github.io/CellBarcode/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Cellular DNA Barcode Analysis toolkit
Description:

The package CellBarcode performs Cellular DNA Barcode analysis. It can handle all kinds of DNA barcodes, as long as the barcode is within a single sequencing read and has a pattern that can be matched by a regular expression. \codeCellBarcode can handle barcodes with flexible lengths, with or without UMI (unique molecular identifier). This tool also can be used for pre-processing some amplicon data such as CRISPR gRNA screening, immune repertoire sequencing, and metagenome data.

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-chronos 1.38.0
Dependencies: pandoc@2.19.2
Propagated dependencies: r-xml@3.99-0.20 r-rjava@1.0-11 r-rcurl@1.98-1.17 r-rbgl@1.86.0 r-openxlsx@4.2.8.1 r-igraph@2.2.1 r-graph@1.88.0 r-foreach@1.5.2 r-doparallel@1.0.17 r-circlize@0.4.16 r-biomart@2.66.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CHRONOS
Licenses: GPL 2
Build system: r
Synopsis: CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis
Description:

This package provides a package used for efficient unraveling of the inherent dynamic properties of pathways. MicroRNA-mediated subpathway topologies are extracted and evaluated by exploiting the temporal transition and the fold change activity of the linked genes/microRNAs.

r-cytopipelinegui 1.8.0
Propagated dependencies: r-shiny@1.11.1 r-plotly@4.11.0 r-ggplot2@4.0.1 r-flowcore@2.22.0 r-cytopipeline@1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://uclouvain-cbio.github.io/CytoPipelineGUI
Licenses: GPL 3
Build system: r
Synopsis: GUI's for visualization of flow cytometry data analysis pipelines
Description:

This package is the companion of the `CytoPipeline` package. It provides GUI's (shiny apps) for the visualization of flow cytometry data analysis pipelines that are run with `CytoPipeline`. Two shiny applications are provided, i.e. an interactive flow frame assessment and comparison tool and an interactive scale transformations visualization and adjustment tool.

r-cytoglmm 1.18.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-strucchange@1.5-4 r-stringr@1.6.0 r-rlang@1.1.6 r-rcolorbrewer@1.1-3 r-pheatmap@1.0.13 r-mbest@0.6.1 r-matrix@1.7-4 r-mass@7.3-65 r-magrittr@2.0.4 r-logging@0.10-108 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-flexmix@2.3-20 r-factoextra@1.0.7 r-dplyr@1.1.4 r-doparallel@1.0.17 r-cowplot@1.2.0 r-caret@7.0-1 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://christofseiler.github.io/CytoGLMM
Licenses: LGPL 3
Build system: r
Synopsis: Conditional Differential Analysis for Flow and Mass Cytometry Experiments
Description:

The CytoGLMM R package implements two multiple regression strategies: A bootstrapped generalized linear model (GLM) and a generalized linear mixed model (GLMM). Most current data analysis tools compare expressions across many computationally discovered cell types. CytoGLMM focuses on just one cell type. Our narrower field of application allows us to define a more specific statistical model with easier to control statistical guarantees. As a result, CytoGLMM finds differential proteins in flow and mass cytometry data while reducing biases arising from marker correlations and safeguarding against false discoveries induced by patient heterogeneity.

r-cellbaser 1.34.0
Propagated dependencies: r-tidyr@1.3.1 r-rsamtools@2.26.0 r-r-utils@2.13.0 r-pbapply@1.7-4 r-jsonlite@2.0.0 r-httr@1.4.7 r-foreach@1.5.2 r-doparallel@1.0.17 r-data-table@1.17.8 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/melsiddieg/cellbaseR
Licenses: ASL 2.0
Build system: r
Synopsis: Querying annotation data from the high performance Cellbase web
Description:

This R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.

r-crisprscoredata 1.14.0
Propagated dependencies: r-experimenthub@3.0.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/crisprVerse/crisprScoreData/issues
Licenses: Expat
Build system: r
Synopsis: Pre-trained models for the crisprScore package
Description:

This package provides an interface to access pre-trained models for on-target and off-target gRNA activity prediction algorithms implemented in the crisprScore package. Pre-trained model data are stored in the ExperimentHub database. Users should consider using the crisprScore package directly to use and load the pre-trained models.

r-cellnoptr 1.56.0
Propagated dependencies: r-xml@3.99-0.20 r-stringr@1.6.0 r-stringi@1.8.7 r-rmarkdown@2.30 r-rgraphviz@2.54.0 r-rcurl@1.98-1.17 r-rbgl@1.86.0 r-igraph@2.2.1 r-graph@1.88.0 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CellNOptR
Licenses: GPL 3
Build system: r
Synopsis: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data
Description:

This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.

r-celda 1.26.0
Propagated dependencies: r-withr@3.0.2 r-uwot@0.2.4 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-singlecellexperiment@1.32.0 r-scran@1.38.0 r-scater@1.38.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rtsne@0.17 r-reshape2@1.4.5 r-rcppeigen@0.3.4.0.2 r-rcpp@1.1.0 r-rcolorbrewer@1.1-3 r-proc@1.19.0.1 r-plyr@1.8.9 r-mcmcprecision@0.4.2 r-matrixstats@1.5.0 r-matrix@1.7-4 r-gtable@0.3.6 r-gridextra@2.3 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-ggdendro@0.2.0 r-foreach@1.5.2 r-enrichr@3.4 r-doparallel@1.0.17 r-digest@0.6.39 r-dendextend@1.19.1 r-delayedarray@0.36.0 r-dbscan@1.2.3 r-data-table@1.17.8 r-complexheatmap@2.26.0 r-circlize@0.4.16
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/celda
Licenses: Expat
Build system: r
Synopsis: CEllular Latent Dirichlet Allocation
Description:

Celda is a suite of Bayesian hierarchical models for clustering single-cell RNA-sequencing (scRNA-seq) data. It is able to perform "bi-clustering" and simultaneously cluster genes into gene modules and cells into cell subpopulations. It also contains DecontX, a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. A variety of scRNA-seq data visualization functions is also included.

r-cafe 1.46.0
Propagated dependencies: r-iranges@2.44.0 r-gridextra@2.3 r-ggplot2@4.0.1 r-ggbio@1.58.0 r-genomicranges@1.62.0 r-biovizbase@1.58.0 r-biobase@2.70.0 r-annotate@1.88.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CAFE
Licenses: GPL 3
Build system: r
Synopsis: Chromosmal Aberrations Finder in Expression data
Description:

Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input.

r-chemminedrugs 1.0.2
Propagated dependencies: r-rsqlite@2.4.4 r-chemminer@3.62.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/ChemmineDrugs
Licenses: Artistic License 2.0
Build system: r
Synopsis: DrugBank data set
Description:

An annotation package for use with ChemmineR. This package includes data from DrugBank. DUD data can be downloaded using the "DUD()" function in ChemmineR.

r-condiments 1.18.0
Propagated dependencies: r-trajectoryutils@1.18.0 r-summarizedexperiment@1.40.0 r-slingshot@2.18.0 r-singlecellexperiment@1.32.0 r-rann@2.6.2 r-pbapply@1.7-4 r-mgcv@1.9-4 r-matrixstats@1.5.0 r-magrittr@2.0.4 r-igraph@2.2.1 r-ecume@0.9.2 r-dplyr@1.1.4 r-distinct@1.22.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://hectorrdb.github.io/condiments/index.html
Licenses: Expat
Build system: r
Synopsis: Differential Topology, Progression and Differentiation
Description:

This package encapsulate many functions to conduct a differential topology analysis. It focuses on analyzing an omic dataset with multiple conditions. While the package is mostly geared toward scRNASeq, it does not place any restriction on the actual input format.

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-crimage 1.58.0
Propagated dependencies: r-sgeostat@1.0-27 r-mass@7.3-65 r-foreach@1.5.2 r-ebimage@4.52.0 r-e1071@1.7-16 r-dnacopy@1.84.0 r-acgh@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CRImage
Licenses: Artistic License 2.0
Build system: r
Synopsis: CRImage a package to classify cells and calculate tumour cellularity
Description:

CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.

r-cleanupdtseq 1.48.0
Propagated dependencies: r-stringr@1.6.0 r-seqinr@4.2-36 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-e1071@1.7-16 r-bsgenome-drerio-ucsc-danrer7@1.4.0 r-bsgenome@1.78.0 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cleanUpdTSeq
Licenses: GPL 2
Build system: r
Synopsis: cleanUpdTSeq cleans up artifacts from polyadenylation sites from oligo(dT)-mediated 3' end RNA sequending data
Description:

This package implements a Naive Bayes classifier for accurately differentiating true polyadenylation sites (pA sites) from oligo(dT)-mediated 3 end sequencing such as PAS-Seq, PolyA-Seq and RNA-Seq by filtering out false polyadenylation sites, mainly due to oligo(dT)-mediated internal priming during reverse transcription. The classifer is highly accurate and outperforms other heuristic methods.

r-cyanofilter 1.18.0
Propagated dependencies: r-mrfdepth@1.0.17 r-ggplot2@4.0.1 r-ggally@2.4.0 r-flowdensity@1.44.0 r-flowcore@2.22.0 r-flowclust@3.48.0 r-cytometree@2.0.6 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/fomotis/cyanoFilter
Licenses: Expat
Build system: r
Synopsis: Phytoplankton Population Identification using Cell Pigmentation and/or Complexity
Description:

An approach to filter out and/or identify phytoplankton cells from all particles measured via flow cytometry pigment and cell complexity information. It does this using a sequence of one-dimensional gates on pre-defined channels measuring certain pigmentation and complexity. The package is especially tuned for cyanobacteria, but will work fine for phytoplankton communities where there is at least one cell characteristic that differentiates every phytoplankton in the community.

r-consica 2.8.0
Propagated dependencies: r-topgo@2.62.0 r-survival@3.8-3 r-summarizedexperiment@1.40.0 r-sm@2.2-6.0 r-rfast@2.1.5.2 r-pheatmap@1.0.13 r-org-hs-eg-db@3.22.0 r-graph@1.88.0 r-go-db@3.22.0 r-ggplot2@4.0.1 r-fastica@1.2-7 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/consICA
Licenses: Expat
Build system: r
Synopsis: consensus Independent Component Analysis
Description:

consICA implements a data-driven deconvolution method – consensus independent component analysis (ICA) to decompose heterogeneous omics data and extract features suitable for patient diagnostics and prognostics. The method separates biologically relevant transcriptional signals from technical effects and provides information about the cellular composition and biological processes. The implementation of parallel computing in the package ensures efficient analysis of modern multicore systems.

r-curatedadiporna 1.26.0
Propagated dependencies: r-summarizedexperiment@1.40.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/MahShaaban/curatedAdipoRNA
Licenses: GPL 3
Build system: r
Synopsis: Curated RNA-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)
Description:

This package provides a curated dataset of RNA-Seq samples. The samples are MDI-induced pre-phagocytes (3T3-L1) at different time points/stage of differentiation. The package document the data collection, pre-processing and processing. In addition to the documentation, the package contains the scripts that was used to generated the data.

r-clstutils 1.58.0
Propagated dependencies: r-rsqlite@2.4.4 r-rjson@0.2.23 r-lattice@0.22-7 r-clst@1.58.0 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/clstutils
Licenses: GPL 3
Build system: r
Synopsis: Tools for performing taxonomic assignment
Description:

This package provides tools for performing taxonomic assignment based on phylogeny using pplacer and clst.

r-cosmic-67 1.46.0
Propagated dependencies: r-variantannotation@1.56.0 r-summarizedexperiment@1.40.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/COSMIC.67
Licenses: GPL 3
Build system: r
Synopsis: COSMIC.67
Description:

COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24).

Total results: 2909