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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-cn-mops 1.56.0
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: http://www.bioinf.jku.at/software/cnmops/cnmops.html
Licenses: LGPL 2.0+
Build system: r
Synopsis: cn.mops - Mixture of Poissons for CNV detection in NGS data
Description:

cn.mops (Copy Number estimation by a Mixture Of PoissonS) is a data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. The package supplies functions to convert BAM files into read count matrices or genomic ranges objects, which are the input objects for cn.mops. cn.mops models the depths of coverage across samples at each genomic position. Therefore, it does not suffer from read count biases along chromosomes. Using a Bayesian approach, cn.mops decomposes read variations across samples into integer copy numbers and noise by its mixture components and Poisson distributions, respectively. cn.mops guarantees a low FDR because wrong detections are indicated by high noise and filtered out. cn.mops is very fast and written in C++.

r-cnvfilter 1.24.0
Propagated dependencies: r-variantannotation@1.56.0 r-summarizedexperiment@1.40.0 r-rsamtools@2.26.0 r-regioner@1.42.0 r-pracma@2.4.6 r-karyoploter@1.36.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-copynumberplots@1.26.0 r-biostrings@2.78.0 r-assertthat@0.2.1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/jpuntomarcos/CNVfilteR
Licenses: Artistic License 2.0
Build system: r
Synopsis: Identifies false positives of CNV calling tools by using SNV calls
Description:

CNVfilteR identifies those CNVs that can be discarded by using the single nucleotide variant (SNV) calls that are usually obtained in common NGS pipelines.

r-chevreulprocess 1.2.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/whtns/chevreulProcess
Licenses: Expat
Build system: r
Synopsis: Tools for managing SingleCellExperiment objects as projects
Description:

This package provides tools for analyzing SingleCellExperiment objects as projects. for input into the chevreulShiny app downstream. Includes functions for analysis of single cell RNA sequencing data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

r-cogena 1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/zhilongjia/cogena
Licenses: LGPL 3
Build system: r
Synopsis: co-expressed gene-set enrichment analysis
Description:

cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.

r-condiments 1.18.0
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-crisprbase 1.14.0
Propagated dependencies: r-stringr@1.6.0 r-s4vectors@0.48.0 r-iranges@2.44.0 r-genomicranges@1.62.0 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/crisprBase
Licenses: Expat
Build system: r
Synopsis: Base functions and classes for CRISPR gRNA design
Description:

This package provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported.

r-cellmig 1.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/snaketron/cellmig
Licenses: FSDG-compatible
Build system: r
Synopsis: Uncertainty-aware quantitative analysis of high-throughput live cell migration data
Description:

High-throughput cell imaging facilitates the analysis of cell migration across many wells treated under different biological conditions. These workflows generate considerable technical noise and biological variability, and therefore technical and biological replicates are necessary, leading to large, hierarchically structured datasets, i.e., cells are nested within technical replicates that are nested within biological replicates. Current statistical analyses of such data usually ignore the hierarchical structure of the data and fail to explicitly quantify uncertainty arising from technical or biological variability. To address this gap, we present cellmig, an R package implementing Bayesian hierarchical models for migration analysis. cellmig quantifies condition- specific velocity changes (e.g., drug effects) while modeling nested data structures and technical artifacts. It further enables synthetic data generation for experimental design optimization.

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-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-cardinal 3.12.1
Propagated dependencies: r-s4vectors@0.48.0 r-protgenerics@1.42.0 r-nlme@3.1-168 r-matter@2.12.0 r-matrix@1.7-4 r-irlba@2.3.5.1 r-ebimage@4.52.0 r-cardinalio@1.8.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: http://www.cardinalmsi.org
Licenses: Artistic License 2.0 FSDG-compatible
Build system: r
Synopsis: mass spectrometry imaging toolbox for statistical analysis
Description:

This package implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.

r-crisprviz 1.12.0
Propagated dependencies: r-txdbmaker@1.6.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-iranges@2.44.0 r-gviz@1.54.0 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 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/crisprViz
Licenses: Expat
Build system: r
Synopsis: Visualization Functions for CRISPR gRNAs
Description:

This package provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.

r-chromdraw 2.40.0
Propagated dependencies: r-rcpp@1.1.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: www.plantcytogenomics.org/chromDraw
Licenses: GPL 3
Build system: r
Synopsis: chromDraw is a R package for drawing the schemes of karyotypes in the linear and circular fashion
Description:

ChromDraw is a R package for drawing the schemes of karyotype(s) in the linear and circular fashion. It is possible to visualized cytogenetic marsk on the chromosomes. This tool has own input data format. Input data can be imported from the GenomicRanges data structure. This package can visualized the data in the BED file format. Here is requirement on to the first nine fields of the BED format. Output files format are *.eps and *.svg.

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-clusterfoldsimilarity 1.6.0
Propagated dependencies: r-singlecellexperiment@1.32.0 r-seuratobject@5.2.0 r-seurat@5.3.1 r-scales@1.4.0 r-reshape2@1.4.5 r-matrix@1.7-4 r-igraph@2.2.1 r-ggplot2@4.0.1 r-ggdendro@0.2.0 r-dplyr@1.1.4 r-cowplot@1.2.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/ClusterFoldSimilarity
Licenses: Artistic License 2.0
Build system: r
Synopsis: Calculate similarity of clusters from different single cell samples using foldchanges
Description:

This package calculates a similarity coefficient using the fold changes of shared features (e.g. genes) among clusters of different samples/batches/datasets. The similarity coefficient is calculated using the dot-product (Hadamard product) of every pairwise combination of Fold Changes between a source cluster i of sample/dataset n and all the target clusters j in sample/dataset m.

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-cellmigration 1.18.0
Propagated dependencies: r-vioplot@0.5.1 r-tiff@0.1-12 r-spatialtools@1.0.5 r-sp@2.2-0 r-reshape2@1.4.5 r-matrixstats@1.5.0 r-hmisc@5.2-4 r-foreach@1.5.2 r-fme@1.3.6.4 r-factominer@2.12 r-doparallel@1.0.17
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/ocbe-uio/cellmigRation/
Licenses: GPL 2
Build system: r
Synopsis: Track Cells, Analyze Cell Trajectories and Compute Migration Statistics
Description:

Import TIFF images of fluorescently labeled cells, and track cell movements over time. Parallelization is supported for image processing and for fast computation of cell trajectories. In-depth analysis of cell trajectories is enabled by 15 trajectory analysis functions.

r-confessdata 1.38.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CONFESSdata
Licenses: GPL 2
Build system: r
Synopsis: Example dataset for CONFESS package
Description:

Example text-converted C01 image files for use in the CONFESS Bioconductor package.

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-copynumberplots 1.26.0
Propagated dependencies: r-variantannotation@1.56.0 r-summarizedexperiment@1.40.0 r-rsamtools@2.26.0 r-rhdf5@2.54.0 r-regioner@1.42.0 r-karyoploter@1.36.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-cn-mops@1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/bernatgel/CopyNumberPlots
Licenses: Artistic License 2.0
Build system: r
Synopsis: Create Copy-Number Plots using karyoploteR functionality
Description:

CopyNumberPlots have a set of functions extending karyoploteRs functionality to create beautiful, customizable and flexible plots of copy-number related data.

r-curatedadipochip 1.26.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/MahShaaban/curatedAdipoChIP
Licenses: GPL 3
Build system: r
Synopsis: Curated ChIP-Seq Dataset of MDI-induced Differentiated Adipocytes (3T3-L1)
Description:

This package provides a curated dataset of publicly available ChIP-sequencing of transcription factors, chromatin remodelers and histone modifications in the 3T3-L1 pre-adipocyte cell line. The package document the data collection, pre-processing and processing of the data. In addition to the documentation, the package contains the scripts that was used to generated the data.

r-cytoviewer 1.10.0
Propagated dependencies: r-viridis@0.6.5 r-svgpanzoom@0.3.4 r-svglite@2.2.2 r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-shinydashboard@0.7.3 r-shinycssloaders@1.1.0 r-shiny@1.11.1 r-s4vectors@0.48.0 r-rcolorbrewer@1.1-3 r-ebimage@4.52.0 r-cytomapper@1.22.0 r-colourpicker@1.3.0 r-archive@1.1.12.1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/BodenmillerGroup/cytoviewer
Licenses: GPL 3
Build system: r
Synopsis: An interactive multi-channel image viewer for R
Description:

This R package supports interactive visualization of multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques using shiny. The cytoviewer interface is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with segmentation masks, integrates well with SingleCellExperiment and SpatialExperiment objects for metadata visualization and supports image downloads.

r-clariomsmousehttranscriptcluster-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/clariomsmousehttranscriptcluster.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix clariomsmouseht annotation data (chip clariomsmousehttranscriptcluster)
Description:

Affymetrix clariomsmouseht annotation data (chip clariomsmousehttranscriptcluster) assembled using data from public repositories.

r-cogps 1.54.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/coGPS
Licenses: GPL 2
Build system: r
Synopsis: cancer outlier Gene Profile Sets
Description:

Gene Set Enrichment Analysis of P-value based statistics for outlier gene detection in dataset merged from multiple studies.

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Total results: 69112