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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-snadata 1.56.0
Propagated dependencies: r-graph@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SNAData
Licenses: LGPL 2.0+
Build system: r
Synopsis: Social Networks Analysis Data Examples
Description:

Data from Wasserman & Faust (1999) "Social Network Analysis".

r-site2target 1.2.0
Propagated dependencies: r-s4vectors@0.48.0 r-mass@7.3-65 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/Site2Target
Licenses: GPL 2
Build system: r
Synopsis: An R package to associate peaks and target genes
Description:

Statistics implemented for both peak-wise and gene-wise associations. In peak-wise associations, the p-value of the target genes of a given set of peaks are calculated. Negative binomial or Poisson distributions can be used for modeling the unweighted peaks targets and log-nromal can be used to model the weighted peaks. In gene-wise associations a table consisting of a set of genes, mapped to specific peaks, is generated using the given rules.

r-singlemoleculefootprintingdata 1.18.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SingleMoleculeFootprintingData
Licenses: GPL 3
Build system: r
Synopsis: Data supporting the SingleMoleculeFootprinting pkg
Description:

This Data package contains data objcets relevanat for the SingleMoleculeFootprinting package. More specifically, it contains one example of aligned sequencing data (.bam & .bai) necessary to run the SingleMoleculeFootprinting vignette. Additionally, we provide data that are essential for some functions to work correctly such as BaitCapture() and SampleCorrelation().

r-signaturesearch 1.24.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/yduan004/signatureSearch/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
Description:

This package implements algorithms and data structures for performing gene expression signature (GES) searches, and subsequently interpreting the results functionally with specialized enrichment methods.

r-sdams 1.30.0
Propagated dependencies: r-trust@0.1-8 r-summarizedexperiment@1.40.0 r-qvalue@2.42.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SDAMS
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: Differential Abundant/Expression Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data
Description:

This Package utilizes a Semi-parametric Differential Abundance/expression analysis (SDA) method for metabolomics and proteomics data from mass spectrometry as well as single-cell RNA sequencing data. SDA is able to robustly handle non-normally distributed data and provides a clear quantification of the effect size.

r-scqtltools 1.2.4
Propagated dependencies: r-yulab-utils@0.2.1 r-vgam@1.1-13 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-singlecellexperiment@1.32.0 r-seuratobject@5.2.0 r-progress@1.2.3 r-patchwork@1.3.2 r-matrix@1.7-4 r-magrittr@2.0.4 r-limma@3.66.0 r-ggplot2@4.0.1 r-gamlss@5.5-0 r-dplyr@1.1.4 r-deseq2@1.50.2 r-biomart@2.66.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/XFWuCN/scQTLtools
Licenses: Expat
Build system: r
Synopsis: scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of single-cell eQTLs
Description:

scQTLtools is a comprehensive R/Bioconductor package that facilitates end-to-end single-cell eQTL analysis, from preprocessing to visualization.

r-svm2crmdata 1.42.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SVM2CRMdata
Licenses: LGPL 2.0+
Build system: r
Synopsis: An example dataset for use with the SVM2CRM package
Description:

An example dataset for use with the SVM2CRM package.

r-scfeatures 1.10.9
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/scFeatures
Licenses: GPL 3
Build system: r
Synopsis: scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction
Description:

scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor.

r-sclcbam 1.42.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SCLCBam
Licenses: GPL 2
Build system: r
Synopsis: Sequence data from chromosome 4 of a small-cell lung tumor
Description:

Whole-exome sequencing data from a murine small-cell lung tumor; only contains data of chromosome 4.

r-snapcount 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/langmead-lab/snapcount
Licenses: Expat
Build system: r
Synopsis: R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
Description:

snapcount is a client interface to the Snaptron webservices which support querying by gene name or genomic region. Results include raw expression counts derived from alignment of RNA-seq samples and/or various summarized measures of expression across one or more regions/genes per-sample (e.g. percent spliced in).

r-scanmir 1.16.0
Propagated dependencies: r-stringi@1.8.7 r-seqlogo@1.76.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-pwalign@1.6.0 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-data-table@1.17.8 r-cowplot@1.2.0 r-biostrings@2.78.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/scanMiR
Licenses: GPL 3
Build system: r
Synopsis: scanMiR
Description:

This package provides a set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3 alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).

r-summix 2.16.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/Summix
Licenses: Expat
Build system: r
Synopsis: Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data
Description:

This package contains the Summix2 method for estimating and adjusting for substructure in genetic summary allele frequency data. The function summix() estimates reference group proportions using a mixture model. The adjAF() function produces adjusted allele frequencies for an observed group with reference group proportions matching a target individual or sample. The summix_local() function estimates local ancestry mixture proportions and performs selection scans in genetic summary data.

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

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

r-schiccompare 1.2.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/dozmorovlab/ScHiCcompare
Licenses: Expat
Build system: r
Synopsis: Differential Analysis of Single-cell Hi-C Data
Description:

This package provides functions for differential chromatin interaction analysis between two single-cell Hi-C data groups. It includes tools for imputation, normalization, and differential analysis of chromatin interactions. The package implements pooling techniques for imputation and offers methods to normalize and test for differential interactions across single-cell Hi-C datasets.

r-seqcombo 1.32.0
Propagated dependencies: r-yulab-utils@0.2.1 r-igraph@2.2.1 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/seqcombo
Licenses: Artistic License 2.0
Build system: r
Synopsis: Visualization Tool for Genetic Reassortment
Description:

This package provides useful functions for visualizing virus reassortment events.

r-spatialsimgp 1.4.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-spatialexperiment@1.20.0 r-mass@7.3-65
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/kinnaryshah/spatialSimGP
Licenses: Expat
Build system: r
Synopsis: Simulate Spatial Transcriptomics Data with the Mean-variance Relationship
Description:

This packages simulates spatial transcriptomics data with the mean- variance relationship using a Gaussian Process model per gene.

r-spaniel 1.24.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-shiny@1.11.1 r-seurat@5.3.1 r-scran@1.38.0 r-scater@1.38.0 r-s4vectors@0.48.0 r-png@0.1-8 r-magrittr@2.0.4 r-jsonlite@2.0.0 r-jpeg@0.1-11 r-igraph@2.2.1 r-ggplot2@4.0.1 r-dropletutils@1.30.0 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/Spaniel
Licenses: Expat
Build system: r
Synopsis: Spatial Transcriptomics Analysis
Description:

Spaniel includes a series of tools to aid the quality control and analysis of Spatial Transcriptomics data. Spaniel can import data from either the original Spatial Transcriptomics system or 10X Visium technology. The package contains functions to create a SingleCellExperiment Seurat object and provides a method of loading a histologial image into R. The spanielPlot function allows visualisation of metrics contained within the S4 object overlaid onto the image of the tissue.

r-sc3 1.38.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/hemberg-lab/SC3
Licenses: GPL 3
Build system: r
Synopsis: Single-Cell Consensus Clustering
Description:

This package provides a tool for unsupervised clustering and analysis of single cell RNA-Seq data.

r-ssrch 1.26.0
Propagated dependencies: r-shiny@1.11.1 r-dt@0.34.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/ssrch
Licenses: Artistic License 2.0
Build system: r
Synopsis: a simple search engine
Description:

Demonstrate tokenization and a search gadget for collections of CSV files.

r-serumstimulation 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/serumStimulation
Licenses: GPL 2+
Build system: r
Synopsis: serumStimulation is a data package which is used by examples in package pcaGoPromoter
Description:

This package contains 13 micro array data results from a serum stimulation experiment.

r-scthi-data 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/scTHI.data
Licenses: GPL 2
Build system: r
Synopsis: The package contains examples of single cell data used in vignettes and examples of the scTHI package; data contain both tumor cells and immune cells from public dataset of glioma
Description:

Data for the vignette and tutorial of the package scTHI.

r-scthi 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/scTHI
Licenses: GPL 2
Build system: r
Synopsis: Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data
Description:

scTHI is an R package to identify active pairs of ligand-receptors from single cells in order to study,among others, tumor-host interactions. scTHI contains a set of signatures to classify cells from the tumor microenvironment.

r-spatialexperimentio 1.2.0
Propagated dependencies: r-spatialexperiment@1.20.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-purrr@1.2.0 r-dropletutils@1.30.0 r-data-table@1.17.8 r-arrow@22.0.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/estellad/SpatialExperimentIO
Licenses: Artistic License 2.0
Build system: r
Synopsis: Read in Xenium, CosMx, MERSCOPE or STARmapPLUS data as SpatialExperiment object
Description:

Read in imaging-based spatial transcriptomics technology data. Current available modules are for Xenium by 10X Genomics, CosMx by Nanostring, MERSCOPE by Vizgen, or STARmapPLUS from Broad Institute. You can choose to read the data in as a SpatialExperiment or a SingleCellExperiment object.

r-singlecelltk 2.20.1
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://www.camplab.net/sctk/
Licenses: Expat
Build system: r
Synopsis: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
Description:

The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general "a la carte" workflow gives users the ability access to multiple methods for data importing, calculation of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering, normalization, batch correction or integration, dimensionality reduction, 2-D embedding, clustering, marker detection, differential expression, cell type labeling, pathway analysis, and data exporting. Curated workflows can be used to run Seurat and Celda. Streamlined quality control can be performed on the command line using the SCTK-QC pipeline. Users can analyze their data using commands in the R console or by using an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire workflows can be summarized and shared with comprehensive HTML reports generated by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk.

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Total results: 69112