_            _    _        _         _
      /\ \         /\ \ /\ \     /\_\      / /\
      \_\ \       /  \ \\ \ \   / / /     / /  \
      /\__ \     / /\ \ \\ \ \_/ / /     / / /\ \__
     / /_ \ \   / / /\ \ \\ \___/ /     / / /\ \___\
    / / /\ \ \ / / /  \ \_\\ \ \_/      \ \ \ \/___/
   / / /  \/_// / /   / / / \ \ \        \ \ \
  / / /      / / /   / / /   \ \ \   _    \ \ \
 / / /      / / /___/ / /     \ \ \ /_/\__/ / /
/_/ /      / / /____\/ /       \ \_\\ \/___/ /
\_\/       \/_________/         \/_/ \_____\/

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-ga4ghclient 1.34.0
Propagated dependencies: r-variantannotation@1.56.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-jsonlite@2.0.0 r-iranges@2.44.0 r-httr@1.4.7 r-genomicranges@1.62.0 r-dplyr@1.1.4 r-biostrings@2.78.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/labbcb/GA4GHclient
Licenses: GPL 2+
Build system: r
Synopsis: Bioconductor package for accessing GA4GH API data servers
Description:

GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.

r-gsca 2.40.0
Propagated dependencies: r-sp@2.2-0 r-shiny@1.11.1 r-rhdf5@2.54.0 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-gplots@3.2.0 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GSCA
Licenses: FSDG-compatible
Build system: r
Synopsis: GSCA: Gene Set Context Analysis
Description:

GSCA takes as input several lists of activated and repressed genes. GSCA then searches through a compendium of publicly available gene expression profiles for biological contexts that are enriched with a specified pattern of gene expression. GSCA provides both traditional R functions and interactive, user-friendly user interface.

r-geosubmission 1.62.0
Propagated dependencies: r-biobase@2.70.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GEOsubmission
Licenses: GPL 2+
Build system: r
Synopsis: Prepares microarray data for submission to GEO
Description:

Helps to easily submit a microarray dataset and the associated sample information to GEO by preparing a single file for upload (direct deposit).

r-gnet2 1.26.0
Propagated dependencies: r-xgboost@1.7.11.1 r-summarizedexperiment@1.40.0 r-reshape2@1.4.5 r-rcpp@1.1.0 r-matrixstats@1.5.0 r-igraph@2.2.1 r-ggplot2@4.0.1 r-dplyr@1.1.4 r-diagrammer@1.0.11
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/chrischen1/GNET2
Licenses: ASL 2.0
Build system: r
Synopsis: Constructing gene regulatory networks from expression data through functional module inference
Description:

Cluster genes to functional groups with E-M process. Iteratively perform TF assigning and Gene assigning, until the assignment of genes did not change, or max number of iterations is reached.

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.

r-guideseq 1.40.0
Propagated dependencies: r-tidyr@1.3.1 r-stringr@1.6.0 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-rlang@1.1.6 r-rio@1.2.4 r-pwalign@1.6.0 r-purrr@1.2.0 r-patchwork@1.3.2 r-openxlsx@4.2.8.1 r-multtest@2.66.0 r-matrixstats@1.5.0 r-limma@3.66.0 r-iranges@2.44.0 r-hash@2.2.6.3 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0 r-genomeinfodb@1.46.0 r-dplyr@1.1.4 r-data-table@1.17.8 r-crisprseek@1.50.0 r-chippeakanno@3.44.0 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GUIDEseq
Licenses: GPL 2+
Build system: r
Synopsis: GUIDE-seq and PEtag-seq analysis pipeline
Description:

The package implements GUIDE-seq and PEtag-seq analysis workflow including functions for filtering UMI and reads with low coverage, obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites with mismatches and indels.

r-gdcrnatools 1.30.0
Propagated dependencies: r-xml@3.99-0.20 r-survminer@0.5.1 r-survival@3.8-3 r-shiny@1.11.1 r-rjson@0.2.23 r-pathview@1.50.0 r-org-hs-eg-db@3.22.0 r-limma@3.66.0 r-jsonlite@2.0.0 r-gplots@3.2.0 r-ggplot2@4.0.1 r-genomicdatacommons@1.34.1 r-edger@4.8.0 r-dt@0.34.0 r-dose@4.4.0 r-deseq2@1.50.2 r-clusterprofiler@4.18.2 r-biomart@2.66.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GDCRNATools
Licenses: Artistic License 2.0
Build system: r
Synopsis: GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data in GDC
Description:

This is an easy-to-use package for downloading, organizing, and integrative analyzing RNA expression data in GDC with an emphasis on deciphering the lncRNA-mRNA related ceRNA regulatory network in cancer. Three databases of lncRNA-miRNA interactions including spongeScan, starBase, and miRcode, as well as three databases of mRNA-miRNA interactions including miRTarBase, starBase, and miRcode are incorporated into the package for ceRNAs network construction. limma, edgeR, and DESeq2 can be used to identify differentially expressed genes/miRNAs. Functional enrichment analyses including GO, KEGG, and DO can be performed based on the clusterProfiler and DO packages. Both univariate CoxPH and KM survival analyses of multiple genes can be implemented in the package. Besides some routine visualization functions such as volcano plot, bar plot, and KM plot, a few simply shiny apps are developed to facilitate visualization of results on a local webpage.

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-genproseq 1.14.0
Propagated dependencies: r-word2vec@0.4.1 r-ttgsea@1.18.0 r-tensorflow@2.20.0 r-reticulate@1.44.1 r-mclust@6.1.2 r-keras@2.16.0 r-deeppincs@1.18.0 r-catencoders@0.1.1
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GenProSeq
Licenses: Artistic License 2.0
Build system: r
Synopsis: Generating Protein Sequences with Deep Generative Models
Description:

Generative modeling for protein engineering is key to solving fundamental problems in synthetic biology, medicine, and material science. Machine learning has enabled us to generate useful protein sequences on a variety of scales. Generative models are machine learning methods which seek to model the distribution underlying the data, allowing for the generation of novel samples with similar properties to those on which the model was trained. Generative models of proteins can learn biologically meaningful representations helpful for a variety of downstream tasks. Furthermore, they can learn to generate protein sequences that have not been observed before and to assign higher probability to protein sequences that satisfy desired criteria. In this package, common deep generative models for protein sequences, such as variational autoencoder (VAE), generative adversarial networks (GAN), and autoregressive models are available. In the VAE and GAN, the Word2vec is used for embedding. The transformer encoder is applied to protein sequences for the autoregressive model.

r-geva 1.18.0
Propagated dependencies: r-matrixstats@1.5.0 r-fastcluster@1.3.0 r-dbscan@1.2.3
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/sbcblab/geva
Licenses: LGPL 3
Build system: r
Synopsis: Gene Expression Variation Analysis (GEVA)
Description:

Statistic methods to evaluate variations of differential expression (DE) between multiple biological conditions. It takes into account the fold-changes and p-values from previous differential expression (DE) results that use large-scale data (*e.g.*, microarray and RNA-seq) and evaluates which genes would react in response to the distinct experiments. This evaluation involves an unique pipeline of statistical methods, including weighted summarization, quantile detection, cluster analysis, and ANOVA tests, in order to classify a subset of relevant genes whose DE is similar or dependent to certain biological factors.

r-generegionscan 1.66.0
Propagated dependencies: r-s4vectors@0.48.0 r-rcolorbrewer@1.1-3 r-biostrings@2.78.0 r-biobase@2.70.0 r-affxparser@1.82.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GeneRegionScan
Licenses: GPL 2+
Build system: r
Synopsis: GeneRegionScan
Description:

This package provides a package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.

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-gse13015 1.18.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-preprocesscore@1.72.0 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/GSE13015
Licenses: FSDG-compatible
Build system: r
Synopsis: GEO accession data GSE13015_GPL6106 as a SummarizedExperiment
Description:

Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015). GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub. This data data could be used as an example supporting BloodGen3Module R package.

r-genomewidesnp5crlmm 1.0.6
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/genomewidesnp5Crlmm
Licenses: Artistic License 2.0
Build system: r
Synopsis: Metadata for fast genotyping with the 'crlmm' package
Description:

Package with metadata for fast genotyping Affymetrix GenomeWideSnp_5 arrays using the crlmm package. Annotation build is hg19.

r-gedi 1.6.1
Propagated dependencies: r-wordcloud2@0.2.1 r-visnetwork@2.1.4 r-tm@0.7-16 r-stringdb@2.22.0 r-simona@1.8.0 r-shinywidgets@0.9.0 r-shinycssloaders@1.1.0 r-shinybs@0.61.1 r-shiny@1.11.1 r-scales@1.4.0 r-rintrojs@0.3.4 r-readxl@1.4.5 r-rcolorbrewer@1.1-3 r-proxyc@0.5.2 r-plotly@4.11.0 r-matrix@1.7-4 r-igraph@2.2.1 r-ggplot2@4.0.1 r-ggdendro@0.2.0 r-fontawesome@0.5.3 r-expm@1.0-0 r-dt@0.34.0 r-dplyr@1.1.4 r-complexheatmap@2.26.0 r-cluster@2.1.8.1 r-circlize@0.4.16 r-bs4dash@2.3.5 r-biocparallel@1.44.0 r-biocneighbors@2.4.0 r-biocfilecache@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/AnnekathrinSilvia/GeDi
Licenses: Expat
Build system: r
Synopsis: Defining and visualizing the distances between different genesets
Description:

The package provides different distances measurements to calculate the difference between genesets. Based on these scores the genesets are clustered and visualized as graph. This is all presented in an interactive Shiny application for easy usage.

r-geneplast-data 0.99.9
Propagated dependencies: r-treeio@1.34.0 r-tidyr@1.3.1 r-tibble@3.3.0 r-readr@2.1.6 r-purrr@1.2.0 r-igraph@2.2.1 r-geneplast@1.36.0 r-dplyr@1.1.4 r-biocfilecache@3.0.0 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.data
Licenses: Artistic License 2.0
Build system: r
Synopsis: Input data for the geneplast package via AnnotationHub
Description:

The package geneplast.data provides datasets from different sources via AnnotationHub to use in geneplast pipelines. The datasets have species, phylogenetic trees, and orthology relationships among eukaryotes from different orthologs databases.

r-gghumanmethcancerpanelv1-db 1.4.1
Propagated dependencies: r-org-hs-eg-db@3.22.0 r-annotationforge@1.52.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GGHumanMethCancerPanelv1.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina Golden Gate Human Methylation Cancer Panel Version 1 annotation data (chip GGHumanMethCancerPanelv1)
Description:

Illumina Golden Gate Human Methylation Cancer Panel Version 1 annotation data (chip GGHumanMethCancerPanelv1) assembled using data from public repositories.

r-gpaexample 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: http://dongjunchung.github.io/GPA/
Licenses: GPL 2+
Build system: r
Synopsis: Example data for the GPA package (Genetic analysis incorporating Pleiotropy and Annotation)
Description:

Example data for the GPA package, consisting of the p-values of 1,219,805 SNPs for five psychiatric disorder GWAS from the psychiatric GWAS consortium (PGC), with the annotation data using genes preferentially expressed in the central nervous system (CNS).

r-grndata 1.42.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/grndata
Licenses: GPL 3
Build system: r
Synopsis: Synthetic Expression Data for Gene Regulatory Network Inference
Description:

Simulated expression data for five large Gene Regulatory Networks from different simulators.

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-gg4way 1.8.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-stringr@1.6.0 r-scales@1.4.0 r-rlang@1.1.6 r-purrr@1.2.0 r-magrittr@2.0.4 r-limma@3.66.0 r-janitor@2.2.1 r-glue@1.8.0 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-edger@4.8.0 r-dplyr@1.1.4 r-deseq2@1.50.2
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/ben-laufer/gg4way
Licenses: Expat
Build system: r
Synopsis: 4way Plots of Differential Expression
Description:

4way plots enable a comparison of the logFC values from two contrasts of differential gene expression. The gg4way package creates 4way plots using the ggplot2 framework and supports popular Bioconductor objects. The package also provides information about the correlation between contrasts and significant genes of interest.

r-geneselectmmd 2.54.0
Propagated dependencies: r-mass@7.3-65 r-limma@3.66.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GeneSelectMMD
Licenses: GPL 2+
Build system: r
Synopsis: Gene selection based on the marginal distributions of gene profiles that characterized by a mixture of three-component multivariate distributions
Description:

Gene selection based on a mixture of marginal distributions.

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-gwas-bayes 1.20.0
Propagated dependencies: r-memoise@2.0.1 r-matrix@1.7-4 r-mass@7.3-65 r-limma@3.66.0 r-ga@3.2.4 r-caret@7.0-1
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GWAS.BAYES
Licenses: FSDG-compatible
Build system: r
Synopsis: Bayesian analysis of Gaussian GWAS data
Description:

This package is built to perform GWAS analysis using Bayesian techniques. Currently, GWAS.BAYES has functionality for the implementation of BICOSS (Williams, J., Ferreira, M. A., and Ji, T. (2022). BICOSS: Bayesian iterative conditional stochastic search for GWAS. BMC Bioinformatics), BGWAS (Williams, J., Xu, S., Ferreira, M. A.. (2023) "BGWAS: Bayesian variable selection in linear mixed models with nonlocal priors for genome-wide association studies." BMC Bioinformatics), and GINA. All methods currently are for the analysis of Gaussian phenotypes The research related to this package was supported in part by National Science Foundation awards DMS 1853549, DMS 1853556, and DMS 2054173.

Total results: 2909