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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-scdblfinder 1.22.0
Propagated dependencies: r-biocgenerics@0.54.0 r-biocneighbors@2.2.0 r-biocparallel@1.42.0 r-biocsingular@1.24.0 r-bluster@1.18.0 r-delayedarray@0.34.1 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-igraph@2.1.4 r-iranges@2.42.0 r-mass@7.3-65 r-matrix@1.7-3 r-rsamtools@2.24.0 r-rtracklayer@1.68.0 r-s4vectors@0.46.0 r-scater@1.36.0 r-scran@1.36.0 r-scuttle@1.18.0 r-singlecellexperiment@1.30.1 r-summarizedexperiment@1.38.1 r-xgboost@1.7.11.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/plger/scDblFinder
Licenses: GPL 3
Synopsis: Detect multiplets in single-cell RNA sequencing data
Description:

The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell RNA sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly found in the scran package, and the new fast and comprehensive scDblFinder method.

r-gtrellis 1.40.0
Propagated dependencies: r-circlize@0.4.16 r-genomicranges@1.60.0 r-getoptlong@1.0.5 r-iranges@2.42.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/jokergoo/gtrellis
Licenses: Expat
Synopsis: Genome level Trellis layout
Description:

Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.

r-nmf 0.28
Propagated dependencies: r-biobase@2.68.0 r-biocmanager@1.30.25 r-bigmemory@4.6.4 r-cluster@2.1.8.1 r-codetools@0.2-20 r-colorspace@2.1-1 r-digest@0.6.37 r-doparallel@1.0.17 r-foreach@1.5.2 r-ggplot2@3.5.2 r-gridbase@0.4-7 r-rcolorbrewer@1.1-3 r-registry@0.5-1 r-reshape2@1.4.4 r-rngtools@1.5.2 r-stringr@1.5.1 r-synchronicity@1.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://renozao.github.io/NMF
Licenses: GPL 2+
Synopsis: Algorithms and framework for nonnegative matrix factorization
Description:

This package provides a framework to perform Non-negative Matrix Factorization (NMF). The package implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new or custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.

r-geneoverlap 1.44.0
Propagated dependencies: r-gplots@3.2.0 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/GeneOverlap/
Licenses: GPL 3
Synopsis: Test and visualize gene overlaps
Description:

This package can be used to test two sets of gene lists and visualize the results.

r-trna 1.26.0
Propagated dependencies: r-biocgenerics@0.54.0 r-biostrings@2.76.0 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-iranges@2.42.0 r-modstrings@1.24.0 r-s4vectors@0.46.0 r-scales@1.4.0 r-stringr@1.5.1 r-structstrings@1.24.0 r-xvector@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/tRNA
Licenses: GPL 3
Synopsis: Analyzing tRNA sequences and structures
Description:

The tRNA package allows tRNA sequences and structures to be accessed and used for subsetting. In addition, it provides visualization tools to compare feature parameters of multiple tRNA sets and correlate them to additional data. The tRNA package uses GRanges objects as inputs requiring only few additional column data sets.

r-ripseeker 1.26.0
Propagated dependencies: r-s4vectors@0.46.0 r-iranges@2.42.0 r-genomicranges@1.60.0 r-summarizedexperiment@1.38.1 r-rsamtools@2.24.0 r-genomicalignments@1.44.0 r-rtracklayer@1.68.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/RIPSeeker
Licenses: GPL 2
Synopsis: Identifying protein-associated transcripts from RIP-seq experiments
Description:

This package infers and discriminates RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.

r-aucell 1.30.1
Propagated dependencies: r-biocgenerics@0.54.0 r-data-table@1.17.4 r-delayedarray@0.34.1 r-delayedmatrixstats@1.30.0 r-gseabase@1.70.0 r-matrix@1.7-3 r-mixtools@2.0.0.1 r-r-utils@2.13.0 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AUCell/
Licenses: GPL 3
Synopsis: Analysis of gene set activity in single-cell RNA-seq data
Description:

AUCell identifies cells with active gene sets (e.g. signatures, gene modules, etc) in single-cell RNA-seq data. AUCell uses the Area Under the Curve (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.

r-motiv 1.43.0
Dependencies: gsl@2.8
Propagated dependencies: r-biocgenerics@0.54.0 r-biostrings@2.76.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-lattice@0.22-7 r-rgadem@2.55.0 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MotIV/
Licenses: GPL 2
Synopsis: Motif identification and validation
Description:

This package is used for the identification and validation of sequence motifs. It makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.

r-adsplit 1.78.0
Propagated dependencies: r-annotationdbi@1.70.0 r-biobase@2.68.0 r-cluster@2.1.8.1 r-go-db@3.21.0 r-keggrest@1.48.0 r-multtest@2.64.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://compdiag.molgen.mpg.de/software/adSplit.shtml
Licenses: GPL 2+
Synopsis: Annotation-driven splits in microarray data
Description:

This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.

r-affyilm 1.60.0
Propagated dependencies: r-affxparser@1.80.0 r-affy@1.86.0 r-biobase@2.68.0 r-gcrma@2.80.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/affyILM
Licenses: GPL 3
Synopsis: Linear model of background subtraction and the Langmuir isotherm
Description:

The affyILM package is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behal of the Langmuir model.

r-systempiper 2.14.1
Propagated dependencies: r-biocgenerics@0.54.0 r-biostrings@2.76.0 r-crayon@1.5.3 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-htmlwidgets@1.6.4 r-magrittr@2.0.3 r-rsamtools@2.24.0 r-s4vectors@0.46.0 r-shortread@1.66.0 r-stringr@1.5.1 r-summarizedexperiment@1.38.1 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/tgirke/systemPipeR
Licenses: Artistic License 2.0
Synopsis: Next generation sequencing workflow and reporting environment
Description:

This R package provides tools for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure.

r-anf 1.30.0
Propagated dependencies: r-biobase@2.68.0 r-igraph@2.1.4 r-mass@7.3-65 r-rcolorbrewer@1.1-3 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ANF
Licenses: GPL 3
Synopsis: Affinity network fusion for complex patient clustering
Description:

The package ANF(Affinity Network Fusion) provides methods for affinity matrix construction and fusion as well as spectral clustering. This package is used for complex patient clustering by integrating multi-omic data through affinity network fusion.

r-gage 2.58.0
Propagated dependencies: r-annotationdbi@1.70.0 r-go-db@3.21.0 r-graph@1.86.0 r-keggrest@1.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-161
Licenses: GPL 2+
Synopsis: Generally applicable gene-set enrichment for pathway analysis
Description:

GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. The gage package provides functions for basic GAGE analysis, result processing and presentation. In addition, it provides demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These functions and data are also useful for gene set analysis using other methods.

r-ggbio 1.56.0
Propagated dependencies: r-annotationdbi@1.70.0 r-annotationfilter@1.32.0 r-biobase@2.68.0 r-biocgenerics@0.54.0 r-biostrings@2.76.0 r-biovizbase@1.56.0 r-bsgenome@1.76.0 r-ensembldb@2.32.0 r-genomeinfodb@1.44.0 r-genomicalignments@1.44.0 r-genomicfeatures@1.60.0 r-genomicranges@1.60.0 r-ggally@2.2.1 r-ggplot2@3.5.2 r-gridextra@2.3 r-gtable@0.3.6 r-hmisc@5.2-3 r-iranges@2.42.0 r-organismdbi@1.50.0 r-reshape2@1.4.4 r-rlang@1.1.6 r-rsamtools@2.24.0 r-rtracklayer@1.68.0 r-s4vectors@0.46.0 r-scales@1.4.0 r-summarizedexperiment@1.38.1 r-variantannotation@1.54.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://www.tengfei.name/ggbio/
Licenses: Artistic License 2.0
Synopsis: Visualization tools for genomic data
Description:

The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.

r-opencyto 2.20.0
Propagated dependencies: r-bh@1.87.0-1 r-biobase@2.68.0 r-biocgenerics@0.54.0 r-cpp11@0.5.2 r-data-table@1.17.4 r-flowclust@3.46.0 r-flowcore@2.20.0 r-flowviz@1.72.0 r-flowworkspace@4.20.0 r-graph@1.86.0 r-ncdfflow@2.54.0 r-rbgl@1.84.0 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/openCyto
Licenses: Artistic License 2.0
Synopsis: Hierarchical gating pipeline for flow cytometry data
Description:

This package is designed to facilitate the automated gating methods in a sequential way to mimic the manual gating strategy.

r-italicsdata 2.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://bioinfo.curie.fr
Licenses: GPL 2+ GPL 3+
Synopsis: ITALICS data
Description:

This package provides data needed to use the ITALICS package.

r-amountain 1.34.0
Dependencies: gsl@2.8
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AMOUNTAIN
Licenses: GPL 2+
Synopsis: Modules for multilayer weighted gene co-expression networks
Description:

This package provides a pure data-driven gene network, WGCN(weighted gene co-expression network) could be constructed only from expression profile. Different layers in such networks may represent different time points, multiple conditions or various species. AMOUNTAIN aims to search active modules in multi-layer WGCN using a continuous optimization approach.

r-italics 2.68.0
Propagated dependencies: r-affxparser@1.80.0 r-dbi@1.2.3 r-glad@2.72.0 r-italicsdata@2.46.0 r-oligo@1.72.0 r-oligoclasses@1.70.0 r-pd-mapping50k-xba240@3.12.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://bioinfo.curie.fr
Licenses: GPL 2
Synopsis: Normalizing of the Affymetrix GeneChip human mapping
Description:

This package provides tools for normalizing and analyzing of GeneChip Mapping 100K and 500K Set. Affymetrix GeneChip Human Mapping 100K and 500K Set allows the DNA copy number mea- surement of respectively 2× 50K and 2× 250K SNPs along the genome. Their high density allows a precise localization of genomic alterations and makes them a powerful tool for cancer and copy number polymorphism study.

r-fdb-infiniummethylation-hg19 2.2.0
Propagated dependencies: r-annotationdbi@1.70.0 r-biostrings@2.76.0 r-genomicfeatures@1.60.0 r-org-hs-eg-db@3.21.0 r-txdb-hsapiens-ucsc-hg19-knowngene@3.2.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/
Licenses: Artistic License 2.0
Synopsis: Compiled HumanMethylation27 and HumanMethylation450 annotations
Description:

This is an annotation package for Illumina Infinium DNA methylation probes. It contains the compiled HumanMethylation27 and HumanMethylation450 annotations.

r-faahko 1.48.1
Propagated dependencies: r-xcms@4.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://dx.doi.org/10.1021/bi0480335
Licenses: LGPL 2.0+
Synopsis: Saghatelian et al. (2004) FAAH knockout LC/MS data
Description:

This package includes positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). It also includes detected peaks in an xcmsSet.

r-animalcules 1.24.0
Propagated dependencies: r-ape@5.8-1 r-assertthat@0.2.1 r-caret@7.0-1 r-covr@3.6.4 r-deseq2@1.48.1 r-dplyr@1.1.4 r-dt@0.33 r-forcats@1.0.0 r-ggforce@0.4.2 r-ggplot2@3.5.2 r-gunifrac@1.8 r-lattice@0.22-7 r-limma@3.64.1 r-magrittr@2.0.3 r-matrix@1.7-3 r-multiassayexperiment@1.34.0 r-plotly@4.10.4 r-rentrez@1.2.3 r-reshape2@1.4.4 r-rocit@2.1.2 r-s4vectors@0.46.0 r-scales@1.4.0 r-shiny@1.10.0 r-shinyjs@2.1.0 r-summarizedexperiment@1.38.1 r-tibble@3.2.1 r-tidyr@1.3.1 r-tsne@0.1-3.1 r-umap@0.2.10.0 r-vegan@2.6-10 r-xml@3.99-0.18
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/compbiomed/animalcules
Licenses: Artistic License 2.0
Synopsis: Interactive microbiome analysis toolkit
Description:

Animalcules is an R package for utilizing up-to-date data analytics, visualization methods, and machine learning models to provide users an easy-to-use interactive microbiome analysis framework. It can be used as a standalone software package or users can explore their data with the accompanying interactive R Shiny application. Traditional microbiome analysis such as alpha/beta diversity and differential abundance analysis are enhanced, while new methods like biomarker identification are introduced by animalcules. Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.

r-timeseriesexperiment 1.13.0
Propagated dependencies: r-deseq2@1.48.1 r-dplyr@1.1.4 r-dynamictreecut@1.63-1 r-edger@4.6.2 r-ggplot2@3.5.2 r-hmisc@5.2-3 r-limma@3.64.1 r-magrittr@2.0.3 r-proxy@0.4-27 r-s4vectors@0.46.0 r-summarizedexperiment@1.38.1 r-tibble@3.2.1 r-tidyr@1.3.1 r-vegan@2.6-10 r-viridis@0.6.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/nlhuong/TimeSeriesExperiment/
Licenses: LGPL 3+
Synopsis: Analysis for short time-series data
Description:

This package is a visualization and analysis toolbox for short time course data which includes dimensionality reduction, clustering, two-sample differential expression testing and gene ranking techniques. The package also provides methods for retrieving enriched pathways.

r-ruvseq 1.42.0
Propagated dependencies: r-biobase@2.68.0 r-edaseq@2.42.0 r-edger@4.6.2 r-mass@7.3-65
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/drisso/RUVSeq
Licenses: Artistic License 2.0
Synopsis: Remove unwanted variation from RNA-Seq data
Description:

This package implements methods to remove unwanted variation (RUV) of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.

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Total results: 45109