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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-gpls 1.82.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/gpls
Licenses: Artistic License 2.0
Build system: r
Synopsis: Classification using generalized partial least squares
Description:

Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.

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-gemini 1.24.0
Propagated dependencies: r-scales@1.4.0 r-pbmcapply@1.5.1 r-mixtools@2.0.0.1 r-magrittr@2.0.4 r-ggplot2@4.0.1 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/gemini
Licenses: Modified BSD
Build system: r
Synopsis: GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens
Description:

GEMINI uses log-fold changes to model sample-dependent and independent effects, and uses a variational Bayes approach to infer these effects. The inferred effects are used to score and identify genetic interactions, such as lethality and recovery. More details can be found in Zamanighomi et al. 2019 (in press).

r-genebreak 1.40.0
Propagated dependencies: r-qdnaseq@1.46.0 r-genomicranges@1.62.0 r-cghcall@2.72.0 r-cghbase@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/stefvanlieshout/GeneBreak
Licenses: GPL 2
Build system: r
Synopsis: Gene Break Detection
Description:

Recurrent breakpoint gene detection on copy number aberration profiles.

r-graphalignment 1.74.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: http://www.thp.uni-koeln.de/~berg/GraphAlignment/
Licenses: FSDG-compatible
Build system: r
Synopsis: GraphAlignment
Description:

Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. (J. Berg and M. Laessig, "Cross-species analysis of biological networks by Bayesian alignment", PNAS 103 (29), 10967-10972 (2006)).

r-genomicdistributions 1.18.0
Propagated dependencies: r-scales@1.4.0 r-reshape2@1.4.5 r-plyr@1.8.9 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-dplyr@1.1.4 r-data-table@1.17.8 r-broom@1.0.10 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: http://code.databio.org/GenomicDistributions
Licenses: FreeBSD
Build system: r
Synopsis: GenomicDistributions: fast analysis of genomic intervals with Bioconductor
Description:

If you have a set of genomic ranges, this package can help you with visualization and comparison. It produces several kinds of plots, for example: Chromosome distribution plots, which visualize how your regions are distributed over chromosomes; feature distance distribution plots, which visualizes how your regions are distributed relative to a feature of interest, like Transcription Start Sites (TSSs); genomic partition plots, which visualize how your regions overlap given genomic features such as promoters, introns, exons, or intergenic regions. It also makes it easy to compare one set of ranges to another.

r-gostag 1.34.0
Propagated dependencies: r-memoise@2.0.1 r-go-db@3.22.0 r-biomart@2.66.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/goSTAG
Licenses: GPL 3
Build system: r
Synopsis: tool to use GO Subtrees to Tag and Annotate Genes within a set
Description:

Gene lists derived from the results of genomic analyses are rich in biological information. For instance, differentially expressed genes (DEGs) from a microarray or RNA-Seq analysis are related functionally in terms of their response to a treatment or condition. Gene lists can vary in size, up to several thousand genes, depending on the robustness of the perturbations or how widely different the conditions are biologically. Having a way to associate biological relatedness between hundreds and thousands of genes systematically is impractical by manually curating the annotation and function of each gene. Over-representation analysis (ORA) of genes was developed to identify biological themes. Given a Gene Ontology (GO) and an annotation of genes that indicate the categories each one fits into, significance of the over-representation of the genes within the ontological categories is determined by a Fisher's exact test or modeling according to a hypergeometric distribution. Comparing a small number of enriched biological categories for a few samples is manageable using Venn diagrams or other means for assessing overlaps. However, with hundreds of enriched categories and many samples, the comparisons are laborious. Furthermore, if there are enriched categories that are shared between samples, trying to represent a common theme across them is highly subjective. goSTAG uses GO subtrees to tag and annotate genes within a set. goSTAG visualizes the similarities between the over-representation of DEGs by clustering the p-values from the enrichment statistical tests and labels clusters with the GO term that has the most paths to the root within the subtree generated from all the GO terms in the cluster.

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-gdnax 1.8.2
Propagated dependencies: r-summarizedexperiment@1.40.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-rcolorbrewer@1.1-3 r-plotrix@3.8-13 r-matrixstats@1.5.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicfiles@1.46.0 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0 r-genomeinfodb@1.46.0 r-cli@3.6.5 r-bitops@1.0-9 r-biostrings@2.78.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-annotationhub@4.0.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/functionalgenomics/gDNAx
Licenses: Artistic License 2.0
Build system: r
Synopsis: Diagnostics for assessing genomic DNA contamination in RNA-seq data
Description:

This package provides diagnostics for assessing genomic DNA contamination in RNA-seq data, as well as plots representing these diagnostics. Moreover, the package can be used to get an insight into the strand library protocol used and, in case of strand-specific libraries, the strandedness of the data. Furthermore, it provides functionality to filter out reads of potential gDNA origin.

r-gsreg 1.44.0
Propagated dependencies: r-org-hs-eg-db@3.22.0 r-homo-sapiens@1.3.1 r-genomicfeatures@1.62.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GSReg
Licenses: GPL 2
Build system: r
Synopsis: Gene Set Regulation (GS-Reg)
Description:

This package provides a package for gene set analysis based on the variability of expressions as well as a method to detect Alternative Splicing Events . It implements DIfferential RAnk Conservation (DIRAC) and gene set Expression Variation Analysis (EVA) methods. For detecting Differentially Spliced genes, it provides an implementation of the Spliced-EVA (SEVA).

r-gdnainrnaseqdata 1.10.0
Propagated dependencies: r-xml@3.99-0.20 r-rsamtools@2.26.0 r-rcurl@1.98-1.17 r-experimenthub@3.0.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/functionalgenomics/gDNAinRNAseqData
Licenses: Artistic License 2.0
Build system: r
Synopsis: RNA-seq data with different levels of gDNA contamination
Description:

This package provides access to BAM files generated from RNA-seq data produced with different levels of gDNA contamination. It currently allows one to download a subset of the data published by Li et al., BMC Genomics, 23:554, 2022. This subset of data is formed by BAM files with about 100,000 alignments with three different levels of gDNA contamination.

r-genomautomorphism 1.12.0
Propagated dependencies: r-xvector@0.50.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-numbers@0.9-2 r-matrixstats@1.5.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-foreach@1.5.2 r-dplyr@1.1.4 r-doparallel@1.0.17 r-data-table@1.17.8 r-biostrings@2.78.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/genomaths/GenomAutomorphism
Licenses: Artistic License 2.0
Build system: r
Synopsis: Compute the automorphisms between DNA's Abelian group representations
Description:

This is a R package to compute the automorphisms between pairwise aligned DNA sequences represented as elements from a Genomic Abelian group. In a general scenario, from genomic regions till the whole genomes from a given population (from any species or close related species) can be algebraically represented as a direct sum of cyclic groups or more specifically Abelian p-groups. Basically, we propose the representation of multiple sequence alignments of length N bp as element of a finite Abelian group created by the direct sum of homocyclic Abelian group of prime-power order.

r-getdee2 1.20.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-htm2txt@2.2.2
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/markziemann/getDEE2
Licenses: GPL 3
Build system: r
Synopsis: Programmatic access to the DEE2 RNA expression dataset
Description:

Digital Expression Explorer 2 (or DEE2 for short) is a repository of processed RNA-seq data in the form of counts. It was designed so that researchers could undertake re-analysis and meta-analysis of published RNA-seq studies quickly and easily. As of April 2020, over 1 million SRA datasets have been processed. This package provides an R interface to access these expression data. More information about the DEE2 project can be found at the project homepage (http://dee2.io) and main publication (https://doi.org/10.1093/gigascience/giz022).

r-goprofiles 1.72.0
Propagated dependencies: r-stringr@1.6.0 r-go-db@3.22.0 r-compquadform@1.4.4 r-biobase@2.70.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/goProfiles
Licenses: GPL 2
Build system: r
Synopsis: goProfiles: an R package for the statistical analysis of functional profiles
Description:

The package implements methods to compare lists of genes based on comparing the corresponding functional profiles'.

r-grenits 1.62.0
Propagated dependencies: r-reshape2@1.4.5 r-rcpparmadillo@15.2.2-1 r-rcpp@1.1.0 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GRENITS
Licenses: GPL 2+
Build system: r
Synopsis: Gene Regulatory Network Inference Using Time Series
Description:

The package offers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection: a linear interaction model, two linear interaction models with added experimental noise (Gaussian and Student distributed) for the case where replicates are available and a non-linear interaction model.

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.

r-gp53cdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/gp53cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: gp53cdf
Description:

This package provides a package containing an environment representing the GP53.CDF file.

r-genemeta 1.82.0
Propagated dependencies: r-genefilter@1.92.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GeneMeta
Licenses: Artistic License 2.0
Build system: r
Synopsis: MetaAnalysis for High Throughput Experiments
Description:

This package provides a collection of meta-analysis tools for analysing high throughput experimental data.

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-geneplast-data-string-v91 0.99.6
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/geneplast.data.string.v91
Licenses: Artistic License 2.0
Build system: r
Synopsis: Input data for the geneplast package
Description:

The package geneplast.data.string.v91 contains input data used in the analysis pipelines available in the geneplast package.

r-gscreend 1.24.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-nloptr@2.2.1 r-fgarch@4052.93 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/imkeller/gscreend
Licenses: GPL 3
Build system: r
Synopsis: Analysis of pooled genetic screens
Description:

Package for the analysis of pooled genetic screens (e.g. CRISPR-KO). The analysis of such screens is based on the comparison of gRNA abundances before and after a cell proliferation phase. The gscreend packages takes gRNA counts as input and allows detection of genes whose knockout decreases or increases cell proliferation.

r-grmetrics 1.36.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-plotly@4.11.0 r-ggplot2@4.0.1 r-drc@3.0-1
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/uc-bd2k/GRmetrics
Licenses: GPL 3
Build system: r
Synopsis: Calculate growth-rate inhibition (GR) metrics
Description:

This package provides functions for calculating and visualizing growth-rate inhibition (GR) metrics.

r-ggsc 1.8.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/YuLab-SMU/ggsc
Licenses: Artistic License 2.0
Build system: r
Synopsis: Visualizing Single Cell and Spatial Transcriptomics
Description:

Useful functions to visualize single cell and spatial data. It supports visualizing Seurat', SingleCellExperiment and SpatialExperiment objects through grammar of graphics syntax implemented in ggplot2'.

Total results: 2909