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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-geneplast 1.36.0
Propagated dependencies: r-snow@0.4-4 r-igraph@2.2.1 r-data-table@1.17.8 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/geneplast
Licenses: GPL 2+
Build system: r
Synopsis: Evolutionary and plasticity analysis of orthologous groups
Description:

Geneplast is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses Shannon information theory and orthologs abundance to estimate the Evolutionary Plasticity Index. Additionally, it implements the Bridge algorithm to determine the evolutionary root of a given gene based on its orthologs distribution.

r-gse103322 1.16.0
Propagated dependencies: r-geoquery@2.78.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GSE103322
Licenses: Artistic License 2.0
Build system: r
Synopsis: GEO accession data GSE103322 as a SingleCellExperiment
Description:

Single cell RNA-Seq data for 5902 cells from 18 patients with oral cavity head and neck squamous cell carcinoma available as GEO accession [GSE103322] (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103322). GSE103322 data have been parsed into a SincleCellExperiment object available in ExperimentHub.

r-gsalightning 1.38.0
Propagated dependencies: r-matrix@1.7-4 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/billyhw/GSALightning
Licenses: FSDG-compatible
Build system: r
Synopsis: Fast Permutation-based Gene Set Analysis
Description:

GSALightning provides a fast implementation of permutation-based gene set analysis for two-sample problem. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation.

r-gem 1.36.0
Propagated dependencies: r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GEM
Licenses: Artistic License 2.0
Build system: r
Synopsis: GEM: fast association study for the interplay of Gene, Environment and Methylation
Description:

This package provides tools for analyzing EWAS, methQTL and GxE genome widely.

r-gatom 1.8.4
Propagated dependencies: r-xml@3.99-0.20 r-sna@2.8 r-shinycyjs@1.0.0 r-plyr@1.8.9 r-network@1.19.0 r-mwcsr@0.1.10 r-intergraph@2.0-4 r-igraph@2.2.1 r-htmlwidgets@1.6.4 r-htmltools@0.5.8.1 r-ggplot2@4.0.1 r-ggally@2.4.0 r-data-table@1.17.8 r-bionet@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/ctlab/gatom/
Licenses: FSDG-compatible
Build system: r
Synopsis: Finding an Active Metabolic Module in Atom Transition Network
Description:

This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.

r-genomicozone 1.24.0
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rdpack@2.6.4 r-plyr@1.8.9 r-lsr@0.5.2 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-ckmeans-1d-dp@4.3.5 r-biomart@2.66.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GenomicOZone
Licenses: FSDG-compatible
Build system: r
Synopsis: Delineate outstanding genomic zones of differential gene activity
Description:

The package clusters gene activity along chromosome into zones, detects differential zones as outstanding, and visualizes maps of outstanding zones across the genome. It enables characterization of effects on multiple genes within adaptive genomic neighborhoods, which could arise from genome reorganization, structural variation, or epigenome alteration. It guarantees cluster optimality, linear runtime to sample size, and reproducibility. One can apply it on genome-wide activity measurements such as copy number, transcriptomic, proteomic, and methylation data.

r-garfield 1.38.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/garfield
Licenses: GPL 3
Build system: r
Synopsis: GWAS Analysis of Regulatory or Functional Information Enrichment with LD correction
Description:

GARFIELD is a non-parametric functional enrichment analysis approach described in the paper GARFIELD: GWAS analysis of regulatory or functional information enrichment with LD correction. Briefly, it is a method that leverages GWAS findings with regulatory or functional annotations (primarily from ENCODE and Roadmap epigenomics data) to find features relevant to a phenotype of interest. It performs greedy pruning of GWAS SNPs (LD r2 > 0.1) and then annotates them based on functional information overlap. Next, it quantifies Fold Enrichment (FE) at various GWAS significance cutoffs and assesses them by permutation testing, while matching for minor allele frequency, distance to nearest transcription start site and number of LD proxies (r2 > 0.8).

r-gsean 1.30.0
Propagated dependencies: r-ppinfer@1.36.0 r-fgsea@1.36.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/gsean
Licenses: Artistic License 2.0
Build system: r
Synopsis: Gene Set Enrichment Analysis with Networks
Description:

Biological molecules in a living organism seldom work individually. They usually interact each other in a cooperative way. Biological process is too complicated to understand without considering such interactions. Thus, network-based procedures can be seen as powerful methods for studying complex process. However, many methods are devised for analyzing individual genes. It is said that techniques based on biological networks such as gene co-expression are more precise ways to represent information than those using lists of genes only. This package is aimed to integrate the gene expression and biological network. A biological network is constructed from gene expression data and it is used for Gene Set Enrichment Analysis.

r-geneclassifiers 1.34.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://doi.org/doi:10.18129/B9.bioc.geneClassifiers
Licenses: GPL 2
Build system: r
Synopsis: Application of gene classifiers
Description:

This packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input.

r-geotcgadata 2.10.0
Propagated dependencies: r-topconfects@1.26.0 r-summarizedexperiment@1.40.0 r-plyr@1.8.9 r-data-table@1.17.8 r-cqn@1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/YuLab-SMU/GeoTcgaData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Processing Various Types of Data on GEO and TCGA
Description:

Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. It's easy to download data from TCGA using the gdc tool, but processing these data into a format suitable for bioinformatics analysis requires more work. This R package was developed to handle these data.

r-gwasurvivr 1.28.0
Propagated dependencies: r-variantannotation@1.56.0 r-survival@3.8-3 r-summarizedexperiment@1.40.0 r-snprelate@1.44.0 r-matrixstats@1.5.0 r-gwastools@1.56.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/suchestoncampbelllab/gwasurvivr
Licenses: Artistic License 2.0
Build system: r
Synopsis: gwasurvivr: an R package for genome wide survival analysis
Description:

gwasurvivr is a package to perform survival analysis using Cox proportional hazard models on imputed genetic data.

r-gdsarray 1.30.0
Propagated dependencies: r-snprelate@1.44.0 r-seqarray@1.50.0 r-s4vectors@0.48.0 r-gdsfmt@1.46.0 r-delayedarray@0.36.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/Bioconductor/GDSArray
Licenses: GPL 3
Build system: r
Synopsis: Representing GDS files as array-like objects
Description:

GDS files are widely used to represent genotyping or sequence data. The GDSArray package implements the `GDSArray` class to represent nodes in GDS files in a matrix-like representation that allows easy manipulation (e.g., subsetting, mathematical transformation) in _R_. The data remains on disk until needed, so that very large files can be processed.

r-ggmanh 1.14.0
Propagated dependencies: r-tidyr@1.3.1 r-seqarray@1.50.0 r-scales@1.4.0 r-rlang@1.1.6 r-rcolorbrewer@1.1-3 r-pals@1.10 r-paletteer@1.6.0 r-magrittr@2.0.4 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-gdsfmt@1.46.0 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/ggmanh
Licenses: Expat
Build system: r
Synopsis: Visualization Tool for GWAS Result
Description:

Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study. The "ggmanh" package aims to keep the generation of these plots simple while maintaining customizability. Main functions include manhattan_plot, qqunif, and thinPoints.

r-gosorensen 1.12.0
Propagated dependencies: r-stringr@1.6.0 r-org-hs-eg-db@3.22.0 r-goprofiles@1.72.0 r-clusterprofiler@4.18.2
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/goSorensen
Licenses: GPL 3
Build system: r
Synopsis: Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)
Description:

This package implements inferential methods to compare gene lists in terms of their biological meaning as expressed in the GO. The compared gene lists are characterized by cross-tabulation frequency tables of enriched GO items. Dissimilarity between gene lists is evaluated using the Sorensen-Dice index. The fundamental guiding principle is that two gene lists are taken as similar if they share a great proportion of common enriched GO items.

r-gwascatdata 0.99.6
Propagated dependencies: r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/gwascatData
Licenses: Artistic License 2.0
Build system: r
Synopsis: text file in cloud with March 30 2021 snapshot of EBI/EMBL GWAS catalog
Description:

This package manages a text file in cloud with March 30 2021 snapshot of EBI/EMBL GWAS catalog.This simplifies access to a snapshot of EBI GWASCAT. More current images can be obtained using the gwascat package.

r-gse159526 1.16.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/wvictor14/GSE159526
Licenses: Expat
Build system: r
Synopsis: Placental cell DNA methylation data from GEO accession GSE159526
Description:

19 term and 9 first trimester placental chorionic villi and matched cell-sorted samples ran on Illumina HumanMethylationEPIC DNA methylation microarrays. This data was made available on GEO accession [GSE159526](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE159526). Both the raw and processed data has been made available on \codeExperimentHub. Raw unprocessed data formatted as an RGChannelSet object for integration and normalization using minfi and other existing Bioconductor packages. Processed normalized data is also available as a DNA methylation \codematrix, with a corresponding phenotype information as a \codedata.frame object.

r-ggspavis 1.16.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-spatialexperiment@1.20.0 r-singlecellexperiment@1.32.0 r-scales@1.4.0 r-rcolorbrewer@1.1-3 r-ggside@0.4.1 r-ggrepel@0.9.6 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/lmweber/ggspavis
Licenses: Expat
Build system: r
Synopsis: Visualization functions for spatial transcriptomics data
Description:

Visualization functions for spatial transcriptomics data. Includes functions to generate several types of plots, including spot plots, feature (molecule) plots, reduced dimension plots, spot-level quality control (QC) plots, and feature-level QC plots, for datasets from the 10x Genomics Visium and other technological platforms. Datasets are assumed to be in either SpatialExperiment or SingleCellExperiment format.

r-genomicdistributionsdata 1.18.0
Propagated dependencies: r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomeinfodb@1.46.0 r-experimenthub@3.0.0 r-ensembldb@2.34.0 r-data-table@1.17.8 r-bsgenome@1.78.0 r-annotationhub@4.0.0 r-annotationfilter@1.34.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GenomicDistributionsData
Licenses: FreeBSD
Build system: r
Synopsis: Reference data for GenomicDistributions package
Description:

This package provides ready to use reference data for GenomicDistributions package. Raw data was obtained from ensembldb and processed with helper functions. Data files are available for the following genome assemblies: hg19, hg38, mm9 and mm10.

r-graphat 1.82.0
Propagated dependencies: r-mcmcpack@1.7-1 r-graph@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GraphAT
Licenses: LGPL 2.0+
Build system: r
Synopsis: Graph Theoretic Association Tests
Description:

This package provides functions and data used in Balasubramanian, et al. (2004).

r-gcrisprtools 2.16.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-robustrankaggreg@1.2.1 r-rmarkdown@2.30 r-limma@3.66.0 r-ggplot2@4.0.1 r-complexheatmap@2.26.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/gCrisprTools
Licenses: Artistic License 2.0
Build system: r
Synopsis: Suite of Functions for Pooled Crispr Screen QC and Analysis
Description:

Set of tools for evaluating pooled high-throughput screening experiments, typically employing CRISPR/Cas9 or shRNA expression cassettes. Contains methods for interrogating library and cassette behavior within an experiment, identifying differentially abundant cassettes, aggregating signals to identify candidate targets for empirical validation, hypothesis testing, and comprehensive reporting. Version 2.0 extends these applications to include a variety of tools for contextualizing and integrating signals across many experiments, incorporates extended signal enrichment methodologies via the "sparrow" package, and streamlines many formal requirements to aid in interpretablity.

r-gatefinder 1.30.0
Propagated dependencies: r-splancs@2.01-45 r-mvoutlier@2.1.1 r-flowfp@1.68.0 r-flowcore@2.22.0 r-diptest@0.77-2
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GateFinder
Licenses: Artistic License 2.0
Build system: r
Synopsis: Projection-based Gating Strategy Optimization for Flow and Mass Cytometry
Description:

Given a vector of cluster memberships for a cell population, identifies a sequence of gates (polygon filters on 2D scatter plots) for isolation of that cell type.

r-gwena 1.20.0
Propagated dependencies: r-wgcna@1.73 r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-rlist@0.4.6.2 r-rcolorbrewer@1.1-3 r-purrr@1.2.0 r-netrep@1.2.9 r-matrixstats@1.5.0 r-magrittr@2.0.4 r-igraph@2.2.1 r-gprofiler2@0.2.4 r-ggplot2@4.0.1 r-dynamictreecut@1.63-1 r-dplyr@1.1.4 r-cluster@2.1.8.1
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GWENA
Licenses: GPL 3
Build system: r
Synopsis: Pipeline for augmented co-expression analysis
Description:

The development of high-throughput sequencing led to increased use of co-expression analysis to go beyong single feature (i.e. gene) focus. We propose GWENA (Gene Whole co-Expression Network Analysis) , a tool designed to perform gene co-expression network analysis and explore the results in a single pipeline. It includes functional enrichment of modules of co-expressed genes, phenotypcal association, topological analysis and comparison of networks configuration between conditions.

r-gep2pep 1.30.0
Propagated dependencies: r-xml@3.99-0.20 r-rhdf5@2.54.0 r-repo@2.1.5 r-iterators@1.0.14 r-gseabase@1.72.0 r-foreach@1.5.2 r-digest@0.6.39 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/gep2pep
Licenses: GPL 3
Build system: r
Synopsis: Creation and Analysis of Pathway Expression Profiles (PEPs)
Description:

Pathway Expression Profiles (PEPs) are based on the expression of pathways (defined as sets of genes) as opposed to individual genes. This package converts gene expression profiles to PEPs and performs enrichment analysis of both pathways and experimental conditions, such as "drug set enrichment analysis" and "gene2drug" drug discovery analysis respectively.

Total results: 2909