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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-easycelltype 1.12.0
Propagated dependencies: r-vctrs@0.6.5 r-rlang@1.1.6 r-org-mm-eg-db@3.22.0 r-org-hs-eg-db@3.22.0 r-magrittr@2.0.4 r-ggplot2@4.0.1 r-forcats@1.0.1 r-dplyr@1.1.4 r-clusterprofiler@4.18.2 r-biocstyle@2.38.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EasyCellType
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotate cell types for scRNA-seq data
Description:

We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA) and a modified versio of Fisher's exact test. The function presents annotation recommendations in graphical outcomes: bar plots for each cluster showing candidate cell types, as well as a dot plot summarizing the top 5 significant annotations for each cluster.

r-expressionatlas 2.2.0
Propagated dependencies: r-xml2@1.5.0 r-xml@3.99-0.20 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rcurl@1.98-1.17 r-limma@3.66.0 r-jsonlite@2.0.0 r-httr@1.4.7 r-biocstyle@2.38.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/ExpressionAtlas
Licenses: GPL 3+
Build system: r
Synopsis: Download datasets from EMBL-EBI Expression Atlas
Description:

This package is for searching for datasets in EMBL-EBI Expression Atlas, and downloading them into R for further analysis. Each Expression Atlas dataset is represented as a SimpleList object with one element per platform. Sequencing data is contained in a SummarizedExperiment object, while microarray data is contained in an ExpressionSet or MAList object.

r-easyrnaseq 2.46.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-shortread@1.68.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-rappdirs@0.3.3 r-lsd@4.1-0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicalignments@1.46.0 r-genomeintervals@1.66.0 r-edger@4.8.0 r-biostrings@2.78.0 r-biomart@2.66.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-biocfilecache@3.0.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/easyRNASeq
Licenses: Artistic License 2.0
Build system: r
Synopsis: Count summarization and normalization for RNA-Seq data
Description:

Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as RPKM or by the DESeq or edgeR package.

r-ewcedata 1.18.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/neurogenomics/ewceData
Licenses: Artistic License 2.0
Build system: r
Synopsis: The ewceData package provides reference data required for ewce
Description:

This package provides reference data required for ewce. Expression Weighted Celltype Enrichment (EWCE) is used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses.

r-escher 1.10.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-spatialexperiment@1.20.0 r-singlecellexperiment@1.32.0 r-rlang@1.1.6 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/boyiguo1/escheR
Licenses: Expat
Build system: r
Synopsis: Unified multi-dimensional visualizations with Gestalt principles
Description:

The creation of effective visualizations is a fundamental component of data analysis. In biomedical research, new challenges are emerging to visualize multi-dimensional data in a 2D space, but current data visualization tools have limited capabilities. To address this problem, we leverage Gestalt principles to improve the design and interpretability of multi-dimensional data in 2D data visualizations, layering aesthetics to display multiple variables. The proposed visualization can be applied to spatially-resolved transcriptomics data, but also broadly to data visualized in 2D space, such as embedding visualizations. We provide this open source R package escheR, which is built off of the state-of-the-art ggplot2 visualization framework and can be seamlessly integrated into genomics toolboxes and workflows.

r-epivizrstandalone 1.38.0
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-git2r@0.36.2 r-genomicfeatures@1.62.0 r-epivizrserver@1.38.0 r-epivizr@2.40.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/epivizrStandalone
Licenses: Expat
Build system: r
Synopsis: Run Epiviz Interactive Genomic Data Visualization App within R
Description:

This package imports the epiviz visualization JavaScript app for genomic data interactive visualization. The epivizrServer package is used to provide a web server running completely within R. This standalone version allows to browse arbitrary genomes through genome annotations provided by Bioconductor packages.

r-erccdashboard 1.44.0
Propagated dependencies: r-stringr@1.6.0 r-scales@1.4.0 r-rocr@1.0-11 r-reshape2@1.4.5 r-qvalue@2.42.0 r-plyr@1.8.9 r-mass@7.3-65 r-locfit@1.5-9.12 r-limma@3.66.0 r-knitr@1.50 r-gtools@3.9.5 r-gridextra@2.3 r-gplots@3.2.0 r-ggplot2@4.0.1 r-edger@4.8.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/erccdashboard
Licenses: FSDG-compatible
Build system: r
Synopsis: Assess Differential Gene Expression Experiments with ERCC Controls
Description:

Technical performance metrics for differential gene expression experiments using External RNA Controls Consortium (ERCC) spike-in ratio mixtures.

r-epitxdb 1.22.0
Propagated dependencies: r-xml2@1.5.0 r-txdbmaker@1.6.0 r-trnadbimport@1.28.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-rex@1.2.1 r-modstrings@1.26.0 r-iranges@2.44.0 r-httr@1.4.7 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-dbi@1.2.3 r-curl@7.0.0 r-biostrings@2.78.0 r-biocgenerics@0.56.0 r-biocfilecache@3.0.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/FelixErnst/EpiTxDb
Licenses: Artistic License 2.0
Build system: r
Synopsis: Storing and accessing epitranscriptomic information using the AnnotationDbi interface
Description:

EpiTxDb facilitates the storage of epitranscriptomic information. More specifically, it can keep track of modification identity, position, the enzyme for introducing it on the RNA, a specifier which determines the position on the RNA to be modified and the literature references each modification is associated with.

r-easyreporting 1.22.0
Propagated dependencies: r-shiny@1.11.1 r-rmarkdown@2.30 r-rlang@1.1.6
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/easyreporting
Licenses: Artistic License 2.0
Build system: r
Synopsis: Helps creating report for improving Reproducible Computational Research
Description:

An S4 class for facilitating the automated creation of rmarkdown files inside other packages/software even without knowing rmarkdown language. Best if implemented in functions as "recursive" style programming.

r-epivizrdata 1.38.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-organismdbi@1.52.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-epivizrserver@1.38.0 r-ensembldb@2.34.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: http://epiviz.github.io
Licenses: Expat
Build system: r
Synopsis: Data Management API for epiviz interactive visualization app
Description:

Serve data from Bioconductor Objects through a WebSocket connection.

r-epitxdb-sc-saccer3 0.99.5
Propagated dependencies: r-epitxdb@1.22.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/FelixErnst/EpiTxDb.Sc.sacCer3
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for EpiTxDb objects
Description:

Exposes an annotation databases generated from several sources by exposing these as EpiTxDb object. Generated for Saccharomyces cerevisiae/sacCer3.

r-enhancerhomologsearch 1.16.0
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rcpp@1.1.0 r-pwalign@1.6.0 r-motifmatchr@1.32.0 r-matrix@1.7-4 r-jsonlite@2.0.0 r-iranges@2.44.0 r-httr@1.4.7 r-genomicranges@1.62.0 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-biocfilecache@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://jianhong.github.io/enhancerHomologSearch
Licenses: GPL 2+
Build system: r
Synopsis: Identification of putative mammalian orthologs to given enhancer
Description:

Get ENCODE data of enhancer region via H3K4me1 peaks and search homolog regions for given sequences. The candidates of enhancer homolog regions can be filtered by distance to target TSS. The top candidates from human and mouse will be aligned to each other and then exported as multiple alignments with given enhancer.

r-edirquery 1.10.0
Propagated dependencies: r-tictoc@1.2.1 r-tibble@3.3.0 r-readr@2.1.6 r-interactionset@1.38.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EDIRquery
Licenses: GPL 3
Build system: r
Synopsis: Query the EDIR Database For Specific Gene
Description:

EDIRquery provides a tool to search for genes of interest within the Exome Database of Interspersed Repeats (EDIR). A gene name is a required input, and users can additionally specify repeat sequence lengths, minimum and maximum distance between sequences, and whether to allow a 1-bp mismatch. Outputs include a summary of results by repeat length, as well as a dataframe of query results. Example data provided includes a subset of the data for the gene GAA (ENSG00000171298). To query the full database requires providing a path to the downloaded database files as a parameter.

r-emdomics 2.40.0
Propagated dependencies: r-preprocesscore@1.72.0 r-matrixstats@1.5.0 r-ggplot2@4.0.1 r-emdist@0.3-3 r-cdft@1.2 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EMDomics
Licenses: Expat
Build system: r
Synopsis: Earth Mover's Distance for Differential Analysis of Genomics Data
Description:

The EMDomics algorithm is used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups. Usually the data will be gene expression values from array-based or sequence-based experiments, but data from other types of experiments can also be analyzed (e.g. copy number variation). Traditional methods like Significance Analysis of Microarrays (SAM) and Linear Models for Microarray Data (LIMMA) use significance tests based on summary statistics (mean and standard deviation) of the distributions. This approach lacks power to identify expression differences between groups that show high levels of intra-group heterogeneity. The Earth Mover's Distance (EMD) algorithm instead computes the "work" needed to transform one distribution into another, thus providing a metric of the overall difference in shape between two distributions. Permutation of sample labels is used to generate q-values for the observed EMD scores. This package also incorporates the Komolgorov-Smirnov (K-S) test and the Cramer von Mises test (CVM), which are both common distribution comparison tests.

r-ebsea 1.38.0
Propagated dependencies: r-empiricalbrownsmethod@1.38.0 r-deseq2@1.50.2
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EBSEA
Licenses: GPL 2
Build system: r
Synopsis: Exon Based Strategy for Expression Analysis of genes
Description:

Calculates differential expression of genes based on exon counts of genes obtained from RNA-seq sequencing data.

r-easierdata 1.16.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-experimenthub@3.0.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/easierData
Licenses: Expat
Build system: r
Synopsis: easier internal data and exemplary dataset from IMvigor210CoreBiologies package
Description:

Access to internal data required for the functional performance of easier package and exemplary bladder cancer dataset with both processed RNA-seq data and information on response to ICB therapy generated by Mariathasan et al. "TGF-B attenuates tumour response to PD-L1 blockade by contributing to exclusion of T cells", published in Nature, 2018 [doi:10.1038/nature25501](https://doi.org/10.1038/nature25501). The data is made available via [`IMvigor210CoreBiologies`](http://research-pub.gene.com/IMvigor210CoreBiologies/) package under the CC-BY license.

r-encodexplorerdata 0.99.5
Propagated dependencies: r-rcurl@1.98-1.17 r-jsonlite@2.0.0 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/ENCODExplorerData
Licenses: Artistic License 2.0
Build system: r
Synopsis: compilation of ENCODE metadata
Description:

This package allows user to quickly access ENCODE project files metadata and give access to helper functions to query the ENCODE rest api, download ENCODE datasets and save the database in SQLite format.

r-epigrahmm 1.18.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-seqinfo@1.0.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rsamtools@2.26.0 r-rhdf5lib@1.32.0 r-rhdf5@2.54.0 r-rcpparmadillo@15.2.2-1 r-rcpp@1.1.0 r-pheatmap@1.0.13 r-matrix@1.7-4 r-mass@7.3-65 r-magrittr@2.0.4 r-limma@3.66.0 r-iranges@2.44.0 r-greylistchip@1.42.0 r-ggpubr@0.6.2 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-data-table@1.17.8 r-csaw@1.44.0 r-bamsignals@1.42.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/epigraHMM
Licenses: Expat
Build system: r
Synopsis: Epigenomic R-based analysis with hidden Markov models
Description:

epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every possible combinatorial pattern of read enrichment across conditions.

r-epimix-data 1.12.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EpiMix.data
Licenses: GPL 3
Build system: r
Synopsis: Data for the EpiMix package
Description:

Supporting data for the EpiMix R package. It include: - HM450_lncRNA_probes.rda - HM450_miRNA_probes.rda - EPIC_lncRNA_probes.rda - EPIC_miRNA_probes.rda - EpigenomeMap.rda - LUAD.sample.annotation - TCGA_BatchData - MET.data - mRNA.data - microRNA.data - lncRNA.data - Sample_EpiMixResults_lncRNA - Sample_EpiMixResults_miRNA - Sample_EpiMixResults_Regular - Sample_EpiMixResults_Enhancer - lncRNA expression data of tumors from TCGA that are stored in the ExperimentHub.

r-egad 1.38.0
Propagated dependencies: r-zoo@1.8-14 r-rcurl@1.98-1.17 r-rcolorbrewer@1.1-3 r-plyr@1.8.9 r-mass@7.3-65 r-limma@3.66.0 r-impute@1.84.0 r-igraph@2.2.1 r-gplots@3.2.0 r-geoquery@2.78.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EGAD
Licenses: GPL 2
Build system: r
Synopsis: Extending guilt by association by degree
Description:

The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods.

r-excluderanges 0.99.10
Propagated dependencies: r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/dozmorovlab/excluderanges
Licenses: Expat
Build system: r
Synopsis: Genomic coordinates of problematic genomic regions
Description:

Genomic coordinates of problematic genomic regions that should be avoided when working with genomic data. GRanges of exclusion regions (formerly known as blacklisted), centromeres, telomeres, known heterochromatin regions, etc. (UCSC gap table data). Primarily for human and mouse genomes, hg19/hg38 and mm9/mm10 genome assemblies.

r-epistasisga 1.12.0
Propagated dependencies: r-survival@3.8-3 r-rcpparmadillo@15.2.2-1 r-rcpp@1.1.0 r-qgraph@1.9.8 r-matrixstats@1.5.0 r-igraph@2.2.1 r-ggplot2@4.0.1 r-data-table@1.17.8 r-biocparallel@1.44.0 r-bigmemory@4.6.4 r-bh@1.87.0-1 r-batchtools@0.9.18
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/mnodzenski/epistasisGA
Licenses: GPL 3
Build system: r
Synopsis: An R package to identify multi-snp effects in nuclear family studies using the GADGETS method
Description:

This package runs the GADGETS method to identify epistatic effects in nuclear family studies. It also provides functions for permutation-based inference and graphical visualization of the results.

r-epitxdb-hs-hg38 0.99.7
Propagated dependencies: r-epitxdb@1.22.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/FelixErnst/EpiTxDb.Hs.hg38
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for EpiTxDb objects
Description:

Exposes an annotation databases generated from several sources by exposing these as EpiTxDb object. Generated for Homo sapiens/hg38.

Total results: 2909