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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-dnashaper 1.38.0
Propagated dependencies: r-rcpp@1.1.0 r-genomicranges@1.62.0 r-fields@17.1 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DNAshapeR
Licenses: GPL 2
Build system: r
Synopsis: High-throughput prediction of DNA shape features
Description:

DNAhapeR is an R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features. The package allows to predict, visualize and encode DNA shape features for statistical learning.

r-deedeeexperiment 1.0.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-limma@3.66.0 r-edger@4.8.0 r-deseq2@1.50.2 r-cli@3.6.5
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://github.com/imbeimainz/DeeDeeExperiment
Licenses: Expat
Build system: r
Synopsis: DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results
Description:

DeeDeeExperiment is an S4 class extending the SingleCellExperiment class, designed to integrate and manage omics analysis results. It introduces two dedicated slots to store Differential Expression Analysis (DEA) results and Functional Enrichment Analysis (FEA) results, providing a structured approach for downstream analysis.

r-epivizrserver 1.38.0
Propagated dependencies: r-rjson@0.2.23 r-r6@2.6.1 r-mime@0.13 r-httpuv@1.6.16
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://epiviz.github.io
Licenses: Expat
Build system: r
Synopsis: WebSocket server infrastructure for epivizr apps and packages
Description:

This package provides objects to manage WebSocket connections to epiviz apps. Other epivizr package use this infrastructure.

r-ecolisakai-db0 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/ecoliSakai.db0
Licenses: Artistic License 2.0
Build system: r
Synopsis: Base Level Annotation databases for E coli Sakai Strain
Description:

Base annotation databases for E coli Sakai Strain, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

r-eopreddata 1.4.0
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/wvictor14/eoPredData
Licenses: Expat
Build system: r
Synopsis: ExperimentHub package containing model data for predicting preeclampsia status for based on plcaental DNA methylation profile
Description:

This package provides access to eoPred pretrained model hosted on ExperimentHub. Model was trained on placental DNA methylation preeclampsia samples using mixOmics splsda. There are two resources: 1. the model object, and 2. a testing data set used to demonstrate the function.

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-epimutacions 1.14.0
Propagated dependencies: r-txdb-hsapiens-ucsc-hg38-knowngene@3.22.0 r-txdb-hsapiens-ucsc-hg19-knowngene@3.22.1 r-txdb-hsapiens-ucsc-hg18-knowngene@3.2.2 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-robustbase@0.99-6 r-reshape2@1.4.5 r-purrr@1.2.0 r-minfi@1.56.0 r-matrixstats@1.5.0 r-isotree@0.6.1-4 r-iranges@2.44.0 r-illuminahumanmethylationepicmanifest@0.3.0 r-illuminahumanmethylationepicanno-ilm10b2-hg19@0.6.0 r-illuminahumanmethylation450kmanifest@0.4.0 r-illuminahumanmethylation450kanno-ilmn12-hg19@0.6.1 r-homo-sapiens@1.3.1 r-gviz@1.54.0 r-gridextra@2.3 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomeinfodb@1.46.0 r-experimenthub@3.0.0 r-epimutacionsdata@1.14.0 r-ensembldb@2.34.0 r-bumphunter@1.52.0 r-biomart@2.66.0 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/e.scm (guix-bioc packages e)
Home page: https://github.com/isglobal-brge/epimutacions
Licenses: Expat
Build system: r
Synopsis: Robust outlier identification for DNA methylation data
Description:

The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations.

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-ensdb-mmusculus-v75 2.99.0
Propagated dependencies: r-ensembldb@2.34.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EnsDb.Mmusculus.v75
Licenses: Artistic License 2.0
Build system: r
Synopsis: Ensembl based annotation package
Description:

Exposes an annotation databases generated from Ensembl.

r-epitxdb-mm-mm10 0.99.6
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.Mm.mm10
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 Mus musculus/mm10.

r-ecoliasv2cdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/ecoliasv2cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: ecoliasv2cdf
Description:

This package provides a package containing an environment representing the Ecoli_ASv2.CDF file.

r-ensdb-rnorvegicus-v75 2.99.0
Propagated dependencies: r-ensembldb@2.34.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EnsDb.Rnorvegicus.v75
Licenses: Artistic License 2.0
Build system: r
Synopsis: Ensembl based annotation package
Description:

Exposes an annotation databases generated from Ensembl.

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-esatac 1.32.0
Propagated dependencies: r-venndiagram@1.7.3 r-tfbstools@1.48.0 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-rmarkdown@2.30 r-rjava@1.0-11 r-rcpp@1.1.0 r-rbowtie2@2.16.0 r-r-utils@2.13.0 r-pipeframe@1.26.0 r-motifmatchr@1.32.0 r-magrittr@2.0.4 r-knitr@1.50 r-jaspar2018@1.1.1 r-iranges@2.44.0 r-igraph@2.2.1 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0 r-digest@0.6.39 r-corrplot@0.95 r-clusterprofiler@4.18.2 r-chipseeker@1.46.1 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocmanager@1.30.27 r-biocgenerics@0.56.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/wzthu/esATAC
Licenses: GPL 3 FSDG-compatible
Build system: r
Synopsis: An Easy-to-use Systematic pipeline for ATACseq data analysis
Description:

This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.

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-easylift 1.8.0
Propagated dependencies: r-rtracklayer@1.70.0 r-r-utils@2.13.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-biocfilecache@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/nahid18/easylift
Licenses: Expat
Build system: r
Synopsis: An R package to perform genomic liftover
Description:

The easylift package provides a convenient tool for genomic liftover operations between different genome assemblies. It seamlessly works with Bioconductor's GRanges objects and chain files from the UCSC Genome Browser, allowing for straightforward handling of genomic ranges across various genome versions. One noteworthy feature of easylift is its integration with the BiocFileCache package. This integration automates the management and caching of chain files necessary for liftover operations. Users no longer need to manually specify chain file paths in their function calls, reducing the complexity of the liftover process.

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-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-etec16s 1.38.0
Propagated dependencies: r-metagenomeseq@1.52.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/etec16s
Licenses: Artistic License 2.0
Build system: r
Synopsis: Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment
Description:

16S rRNA gene sequencing data to study changes in the faecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin.

r-extrachips 1.14.2
Propagated dependencies: r-vctrs@0.6.5 r-tidyselect@1.2.1 r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 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-rlang@1.1.6 r-rcolorbrewer@1.1-3 r-patchwork@1.3.2 r-matrixstats@1.5.0 r-iranges@2.44.0 r-interactionset@1.38.0 r-glue@1.8.0 r-ggside@0.4.1 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-forcats@1.0.1 r-edger@4.8.0 r-dplyr@1.1.4 r-csaw@1.44.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/smped/extraChIPs
Licenses: GPL 3
Build system: r
Synopsis: Additional functions for working with ChIP-Seq data
Description:

This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented.

r-epiregulon 2.0.2
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-scuttle@1.20.0 r-scrapper@1.4.0 r-scran@1.38.0 r-s4vectors@0.48.0 r-rcpp@1.1.0 r-motifmatchr@1.32.0 r-matrix@1.7-4 r-lifecycle@1.0.4 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-experimenthub@3.0.0 r-entropy@1.3.2 r-checkmate@2.3.3 r-bsgenome-mmusculus-ucsc-mm10@1.4.3 r-bsgenome-hsapiens-ucsc-hg38@1.4.5 r-bsgenome-hsapiens-ucsc-hg19@1.4.3 r-biocparallel@1.44.0 r-annotationhub@4.0.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/xiaosaiyao/epiregulon/
Licenses: Expat
Build system: r
Synopsis: Gene regulatory network inference from single cell epigenomic data
Description:

Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.

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-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.

Total results: 2909