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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-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-gothic 1.46.0
Propagated dependencies: r-shortread@1.68.0 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-ggplot2@4.0.1 r-genomicranges@1.62.0 r-data-table@1.17.8 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocmanager@1.30.27 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GOTHiC
Licenses: GPL 3
Build system: r
Synopsis: Binomial test for Hi-C data analysis
Description:

This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome.

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-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-ga4ghshiny 1.32.0
Propagated dependencies: r-tidyr@1.3.1 r-shinythemes@1.2.0 r-shinyjs@2.1.0 r-shiny@1.11.1 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-purrr@1.2.0 r-openxlsx@4.2.8.1 r-genomicfeatures@1.62.0 r-genomeinfodb@1.46.0 r-ga4ghclient@1.34.0 r-dt@0.34.0 r-dplyr@1.1.4 r-biocgenerics@0.56.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/labbcb/GA4GHshiny
Licenses: GPL 3
Build system: r
Synopsis: Shiny application for interacting with GA4GH-based data servers
Description:

GA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network.

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-genomicsupersignature 1.18.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-plotly@4.11.0 r-irlba@2.3.5.1 r-ggpubr@0.6.2 r-ggplot2@4.0.1 r-flextable@0.9.10 r-dplyr@1.1.4 r-complexheatmap@2.26.0 r-biocfilecache@3.0.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/shbrief/GenomicSuperSignature
Licenses: Artistic License 2.0
Build system: r
Synopsis: Interpretation of RNA-seq experiments through robust, efficient comparison to public databases
Description:

This package provides a novel method for interpreting new transcriptomic datasets through near-instantaneous comparison to public archives without high-performance computing requirements. Through the pre-computed index, users can identify public resources associated with their dataset such as gene sets, MeSH term, and publication. Functions to identify interpretable annotations and intuitive visualization options are implemented in this package.

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-generxcluster 1.46.0
Propagated dependencies: r-iranges@2.44.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/geneRxCluster
Licenses: GPL 2+
Build system: r
Synopsis: gRx Differential Clustering
Description:

Detect Differential Clustering of Genomic Sites such as gene therapy integrations. The package provides some functions for exploring genomic insertion sites originating from two different sources. Possibly, the two sources are two different gene therapy vectors. Vectors are preferred that target sensitive regions less frequently, motivating the search for localized clusters of insertions and comparison of the clusters formed by integration of different vectors. Scan statistics allow the discovery of spatial differences in clustering and calculation of False Discovery Rates (FDRs) providing statistical methods for comparing retroviral vectors. A scan statistic for comparing two vectors using multiple window widths to detect clustering differentials and compute FDRs is implemented here.

r-gigseadata 1.28.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GIGSEAdata
Licenses: LGPL 3
Build system: r
Synopsis: Gene set collections for the GIGSEA package
Description:

The gene set collection used for the GIGSEA package.

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-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-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-genesummary 0.99.6
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://github.com/jokergoo/GeneSummary
Licenses: Expat
Build system: r
Synopsis: RefSeq Gene Summaries
Description:

This package provides long description of genes collected from the RefSeq database. The text in "COMMENT" section started with "Summary" is extracted as the description of the gene. The long text descriptions can be used for analysis such as text mining.

r-gotools 1.84.0
Propagated dependencies: r-go-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/goTools
Licenses: GPL 2
Build system: r
Synopsis: Functions for Gene Ontology database
Description:

Wraper functions for description/comparison of oligo ID list using Gene Ontology database.

r-gmrp 1.38.0
Propagated dependencies: r-plotrix@3.8-13 r-genomicranges@1.62.0 r-diagram@1.6.5
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GMRP
Licenses: GPL 2+
Build system: r
Synopsis: GWAS-based Mendelian Randomization and Path Analyses
Description:

Perform Mendelian randomization analysis of multiple SNPs to determine risk factors causing disease of study and to exclude confounding variabels and perform path analysis to construct path of risk factors to the disease.

r-gmicr 1.24.0
Propagated dependencies: r-wgcna@1.73 r-shiny@1.11.1 r-reshape2@1.4.5 r-org-mm-eg-db@3.22.0 r-org-hs-eg-db@3.22.0 r-gseabase@1.72.0 r-grbase@2.0.3 r-grain@1.4.5 r-gostats@2.76.0 r-foreach@1.5.2 r-dt@0.34.0 r-doparallel@1.0.17 r-data-table@1.17.8 r-category@2.76.0 r-bnlearn@5.1 r-ape@5.8-1 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GmicR
Licenses: FSDG-compatible
Build system: r
Synopsis: Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)
Description:

This package uses bayesian network learning to detect relationships between Gene Modules detected by WGCNA and immune cell signatures defined by xCell. It is a hypothesis generating tool.

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-gsri 2.58.0
Propagated dependencies: r-les@1.60.0 r-gseabase@1.72.0 r-genefilter@1.92.0 r-fdrtool@1.2.18 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GSRI
Licenses: GPL 3
Build system: r
Synopsis: Gene Set Regulation Index
Description:

The GSRI package estimates the number of differentially expressed genes in gene sets, utilizing the concept of the Gene Set Regulation Index (GSRI).

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-gsbenchmark 1.30.0
Channel: guix-bioc
Location: guix-bioc/packages/g.scm (guix-bioc packages g)
Home page: https://bioconductor.org/packages/GSBenchMark
Licenses: GPL 2
Build system: r
Synopsis: Gene Set Benchmark
Description:

Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al.

r-ginmapper 1.6.0
Propagated dependencies: r-xml@3.99-0.20 r-uniprot-ws@2.50.0 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-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.

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.

Total results: 2909