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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-ginmapper 1.6.0
Propagated dependencies: r-xml@3.99-0.20 r-uniprot-ws@2.50.1 r-rvest@1.0.5 r-rentrez@1.2.4 r-memoise@2.0.1 r-keggrest@1.50.0 r-jsonlite@2.0.0 r-httr@1.4.7 r-cachem@1.1.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/ginmappeR
Licenses: FSDG-compatible
Build system: r
Synopsis: Gene Identifier Mapper
Description:

This package provides functionalities to translate gene or protein identifiers between state-of-art biological databases: CARD (<https://card.mcmaster.ca/>), NCBI Protein, Nucleotide and Gene (<https://www.ncbi.nlm.nih.gov/>), UniProt (<https://www.uniprot.org/>) and KEGG (<https://www.kegg.jp>). Also offers complementary functionality like NCBI identical proteins or UniProt similar genes clusters retrieval.

r-gg4way 1.8.0
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-gaschyhs 1.48.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: http://genome-www.stanford.edu/yeast_stress/data/rawdata/complete_dataset.txt
Licenses: Artistic License 2.0
Build system: r
Synopsis: ExpressionSet for response of yeast to heat shock and other environmental stresses
Description:

Data from PMID 11102521.

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-gcrisprtools 2.16.0
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-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-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-genomicplot 1.8.1
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/shuye2009/GenomicPlot
Licenses: GPL 2
Build system: r
Synopsis: Plot profiles of next generation sequencing data in genomic features
Description:

Visualization of next generation sequencing (NGS) data is essential for interpreting high-throughput genomics experiment results. GenomicPlot facilitates plotting of NGS data in various formats (bam, bed, wig and bigwig); both coverage and enrichment over input can be computed and displayed with respect to genomic features (such as UTR, CDS, enhancer), and user defined genomic loci or regions. Statistical tests on signal intensity within user defined regions of interest can be performed and represented as boxplots or bar graphs. Parallel processing is used to speed up computation on multicore platforms. In addition to genomic plots which is suitable for displaying of coverage of genomic DNA (such as ChIPseq data), metagenomic (without introns) plots can also be made for RNAseq or CLIPseq data as well.

r-gcapc 1.34.0
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-matrixstats@1.5.0 r-mass@7.3-65 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicalignments@1.46.0 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://github.com/tengmx/gcapc
Licenses: GPL 3
Build system: r
Synopsis: GC Aware Peak Caller
Description:

Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.

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-gdrcore 1.8.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-s4vectors@0.48.0 r-purrr@1.2.0 r-multiassayexperiment@1.36.1 r-gdrutils@1.8.0 r-futile-logger@1.4.3 r-data-table@1.17.8 r-checkmate@2.3.3 r-bumpymatrix@1.18.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/gdrplatform/gDRcore
Licenses: Artistic License 2.0
Build system: r
Synopsis: Processing functions and interface to process and analyze drug dose-response data
Description:

This package contains core functions to process and analyze drug response data. The package provides tools for normalizing, averaging, and calculation of gDR metrics data. All core functions are wrapped into the pipeline function allowing analyzing the data in a straightforward way.

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-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-g4snvhunter 1.2.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/rongxinzh/G4SNVHunter
Licenses: Expat
Build system: r
Synopsis: Evaluating SNV-Induced Disruption of G-Quadruplex Structures
Description:

G-quadruplexes (G4s) are unique nucleic acid secondary structures predominantly found in guanine-rich regions and have been shown to be involved in various biological regulatory processes. G4SNVHunter is an R package designed to rapidly identify genomic sequences with G4-forming propensity and to accurately screen user-provided single nucleotide variants—as well as other small-scale variants such as indels and MNVs—for their potential to destabilize these structures. This allows researchers to then screen these critical variants for deeper study, digging into how they might influence biological functions—think gene regulation, for instance—by impairing G4 formation propensity.

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-genestructuretools 1.30.0
Propagated dependencies: r-stringr@1.6.0 r-stringdist@0.9.15 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-plyr@1.8.9 r-iranges@2.44.0 r-gviz@1.54.0 r-genomicranges@1.62.0 r-data-table@1.17.8 r-bsgenome-mmusculus-ucsc-mm10@1.4.3 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GeneStructureTools
Licenses: Modified BSD
Build system: r
Synopsis: Tools for spliced gene structure manipulation and analysis
Description:

GeneStructureTools can be used to create in silico alternative splicing events, and analyse potential effects this has on functional gene products.

r-geneattribution 1.36.0
Propagated dependencies: r-seqinfo@1.0.0 r-rtracklayer@1.70.0 r-org-hs-eg-db@3.22.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicfeatures@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/geneAttribution
Licenses: Artistic License 2.0
Build system: r
Synopsis: Identification of candidate genes associated with genetic variation
Description:

Identification of the most likely gene or genes through which variation at a given genomic locus in the human genome acts. The most basic functionality assumes that the closer gene is to the input locus, the more likely the gene is to be causative. Additionally, any empirical data that links genomic regions to genes (e.g. eQTL or genome conformation data) can be used if it is supplied in the UCSC .BED file format.

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-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-glmsparsenet 1.28.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://www.github.com/sysbiomed/glmSparseNet
Licenses: GPL 3
Build system: r
Synopsis: Network Centrality Metrics for Elastic-Net Regularized Models
Description:

glmSparseNet is an R-package that generalizes sparse regression models when the features (e.g. genes) have a graph structure (e.g. protein-protein interactions), by including network-based regularizers. glmSparseNet uses the glmnet R-package, by including centrality measures of the network as penalty weights in the regularization. The current version implements regularization based on node degree, i.e. the strength and/or number of its associated edges, either by promoting hubs in the solution or orphan genes in the solution. All the glmnet distribution families are supported, namely "gaussian", "poisson", "binomial", "multinomial", "cox", and "mgaussian".

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-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-geneplast 1.36.0
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-ggtreespace 1.6.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/YuLab-SMU/ggtreeSpace
Licenses: Artistic License 2.0
Build system: r
Synopsis: Visualizing Phylomorphospaces using 'ggtree'
Description:

This package is a comprehensive visualization tool specifically designed for exploring phylomorphospace. It not only simplifies the process of generating phylomorphospace, but also enhances it with the capability to add graphic layers to the plot with grammar of graphics to create fully annotated phylomorphospaces. It also provide some utilities to help interpret evolutionary patterns.

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Total results: 69112