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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-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-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-genextender 1.36.0
Propagated dependencies: r-wordcloud@2.6 r-tm@0.7-16 r-snowballc@0.7.1 r-rtracklayer@1.70.0 r-rcolorbrewer@1.1-3 r-org-rn-eg-db@3.22.0 r-networkd3@0.4.1 r-go-db@3.22.0 r-dplyr@1.1.4 r-data-table@1.17.8 r-biocstyle@2.38.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/Bohdan-Khomtchouk/geneXtendeR
Licenses: GPL 3+
Build system: r
Synopsis: Optimized Functional Annotation Of ChIP-seq Data
Description:

geneXtendeR optimizes the functional annotation of ChIP-seq peaks by exploring relative differences in annotating ChIP-seq peak sets to variable-length gene bodies. In contrast to prior techniques, geneXtendeR considers peak annotations beyond just the closest gene, allowing users to see peak summary statistics for the first-closest gene, second-closest gene, ..., n-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene's coordinates. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process. As such, the goal of geneXtendeR is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR.

r-grasp2db 1.1.1
Propagated dependencies: r-seqinfo@1.0.0 r-rsqlite@2.4.4 r-genomeinfodb@1.46.0 r-dplyr@1.1.4 r-digest@0.6.39 r-dbplyr@2.5.1 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/grasp2db
Licenses: FSDG-compatible
Build system: r
Synopsis: grasp2db, sqlite wrap of GRASP 2.0
Description:

grasp2db, sqlite wrap of NHLBI GRASP 2.0, an extended GWAS catalog.

r-genomeintervals 1.66.0
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-iranges@2.44.0 r-intervals@0.15.5 r-genomicranges@1.62.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/genomeIntervals
Licenses: Artistic License 2.0
Build system: r
Synopsis: Operations on genomic intervals
Description:

This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package girafe'.

r-gdrimport 1.8.1
Propagated dependencies: r-yaml@2.3.10 r-xml@3.99-0.20 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringi@1.8.7 r-s4vectors@0.48.0 r-rio@1.2.4 r-readxl@1.4.5 r-pharmacogx@3.14.0 r-openxlsx@4.2.8.1 r-multiassayexperiment@1.36.1 r-magrittr@2.0.4 r-gdrutils@1.8.0 r-futile-logger@1.4.3 r-data-table@1.17.8 r-coregx@2.14.0 r-checkmate@2.3.3 r-bumpymatrix@1.18.0 r-assertthat@0.2.1
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/gdrplatform/gDRimport
Licenses: Artistic License 2.0
Build system: r
Synopsis: Package for handling the import of dose-response data
Description:

The package is a part of the gDR suite. It helps to prepare raw drug response data for downstream processing. It mainly contains helper functions for importing/loading/validating dose-response data provided in different file formats.

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-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-gopro 1.36.0
Propagated dependencies: r-s4vectors@0.48.0 r-rcpp@1.1.0 r-org-hs-eg-db@3.22.0 r-multiassayexperiment@1.36.1 r-iranges@2.44.0 r-go-db@3.22.0 r-foreach@1.5.2 r-doparallel@1.0.17 r-dendextend@1.19.1 r-bh@1.87.0-1 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/mi2-warsaw/GOpro
Licenses: GPL 3
Build system: r
Synopsis: Find the most characteristic gene ontology terms for groups of human genes
Description:

Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 Group (http://mi2.mini.pw.edu.pl/, https://github.com/geneticsMiNIng).

r-generecommender 1.82.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/geneRecommender
Licenses: GPL 2+
Build system: r
Synopsis: gene recommender algorithm to identify genes coexpressed with a query set of genes
Description:

This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions.

r-gse62944 1.38.0
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: http://bioconductor.org/packages/release/bioc/html/GSE62944.html
Licenses: Artistic License 2.0
Build system: r
Synopsis: GEO accession data GSE62944 as a SummarizedExperiment
Description:

TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub.

r-graper 1.26.0
Propagated dependencies: r-rcpparmadillo@15.2.2-1 r-rcpp@1.1.0 r-matrixstats@1.5.0 r-matrix@1.7-4 r-ggplot2@4.0.1 r-cowplot@1.2.0 r-bh@1.87.0-1
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/graper
Licenses: GPL 2+
Build system: r
Synopsis: Adaptive penalization in high-dimensional regression and classification with external covariates using variational Bayes
Description:

This package enables regression and classification on high-dimensional data with different relative strengths of penalization for different feature groups, such as different assays or omic types. The optimal relative strengths are chosen adaptively. Optimisation is performed using a variational Bayes approach.

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-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-genefu 2.42.0
Propagated dependencies: r-survcomp@1.60.0 r-mclust@6.1.2 r-limma@3.66.0 r-impute@1.84.0 r-ic10trainingdata@2.0.1 r-ic10@2.0.2 r-biomart@2.66.0 r-amap@0.8-20 r-aims@1.42.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: http://www.pmgenomics.ca/bhklab/software/genefu
Licenses: Artistic License 2.0
Build system: r
Synopsis: Computation of Gene Expression-Based Signatures in Breast Cancer
Description:

This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival 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-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-gmapr 1.51.1
Dependencies: zlib@1.3.1
Propagated dependencies: r-variantannotation@1.56.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rsamtools@2.26.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocparallel@1.44.0 r-biocio@1.20.0 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://bioconductor.org/packages/gmapR
Licenses: Artistic License 2.0
Build system: r
Synopsis: An R interface to the GMAP/GSNAP/GSTRUCT suite
Description:

GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.

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-gigsea 1.28.0
Propagated dependencies: r-matrix@1.7-4 r-mass@7.3-65 r-locfdr@1.1-8
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GIGSEA
Licenses: LGPL 3
Build system: r
Synopsis: Genotype Imputed Gene Set Enrichment Analysis
Description:

We presented the Genotype-imputed Gene Set Enrichment Analysis (GIGSEA), a novel method that uses GWAS-and-eQTL-imputed trait-associated differential gene expression to interrogate gene set enrichment for the trait-associated SNPs. By incorporating eQTL from large gene expression studies, e.g. GTEx, GIGSEA appropriately addresses such challenges for SNP enrichment as gene size, gene boundary, SNP distal regulation, and multiple-marker regulation. The weighted linear regression model, taking as weights both imputation accuracy and model completeness, was used to perform the enrichment test, properly adjusting the bias due to redundancy in different gene sets. The permutation test, furthermore, is used to evaluate the significance of enrichment, whose efficiency can be largely elevated by expressing the computational intensive part in terms of large matrix operation. We have shown the appropriate type I error rates for GIGSEA (<5%), and the preliminary results also demonstrate its good performance to uncover the real signal.

r-genarise 1.86.0
Propagated dependencies: r-xtable@1.8-4 r-tkrplot@0.0-30 r-locfit@1.5-9.12
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: http://www.ifc.unam.mx/genarise
Licenses: FSDG-compatible
Build system: r
Synopsis: Microarray Analysis tool
Description:

genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.

r-geuvadistranscriptexpr 1.38.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GeuvadisTranscriptExpr
Licenses: GPL 3+
Build system: r
Synopsis: Data package with transcript expression and bi-allelic genotypes from the GEUVADIS project
Description:

This package provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from the GEUVADIS project, Lappalainen et al.

r-genomicinstability 1.16.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-mixtools@2.0.0.1 r-checkmate@2.3.3
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/DarwinHealth/genomicInstability
Licenses: FSDG-compatible
Build system: r
Synopsis: Genomic Instability estimation for scRNA-Seq
Description:

This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. GIA estimates the association between gene expression and genomic location of the coding genes. It uses the aREA algorithm to quantify the enrichment of sets of contiguous genes (loci-blocks) on the gene expression profiles and estimates the Genomic Instability Score (GIS) for each analyzed cell.

r-grafgen 1.6.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-stringr@1.6.0 r-shiny@1.11.1 r-scales@1.4.0 r-rlang@1.1.6 r-rcolorbrewer@1.1-3 r-plotly@4.11.0 r-ggpubr@0.6.2 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-dplyr@1.1.4 r-cowplot@1.2.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GrafGen
Licenses: GPL 2
Build system: r
Synopsis: Classification of Helicobacter Pylori Genomes
Description:

To classify Helicobacter pylori genomes according to genetic distance from nine reference populations. The nine reference populations are hpgpAfrica, hpgpAfrica-distant, hpgpAfroamerica, hpgpEuroamerica, hpgpMediterranea, hpgpEurope, hpgpEurasia, hpgpAsia, and hpgpAklavik86-like. The vertex populations are Africa, Europe and Asia.

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Total results: 68658