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r-ecolileucine 1.50.0
Propagated dependencies: r-ecolicdf@2.18.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/ecoliLeucine
Licenses: GPL 2+
Build system: r
Synopsis: Experimental data with Affymetrix E. coli chips
Description:

Experimental data with Affymetrix E. coli chips, as reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield, J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25, 2002.

r-eatonetalchipseq 0.48.0
Propagated dependencies: r-shortread@1.68.0 r-rtracklayer@1.70.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EatonEtAlChIPseq
Licenses: FSDG-compatible
Build system: r
Synopsis: ChIP-seq data of ORC-binding sites in Yeast excerpted from Eaton et al. 2010
Description:

ChIP-seq analysis subset from "Conserved nucleosome positioning defines replication origins" (PMID 20351051).

r-epivizr 2.40.0
Propagated dependencies: r-s4vectors@0.48.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-epivizrserver@1.38.0 r-epivizrdata@1.38.0 r-bumphunter@1.52.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/epivizr
Licenses: Artistic License 2.0
Build system: r
Synopsis: R Interface to epiviz web app
Description:

This package provides connections to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and RangedSummarizedExperiment objects), while providing an easy mechanism to support other data structures (through package epivizrData). Visualizations (using d3.js) can be easily added to the web app as well.

r-enrichviewnet 1.8.1
Propagated dependencies: r-stringr@1.6.0 r-strex@2.0.1 r-reshape2@1.4.5 r-rcy3@2.30.0 r-jsonlite@2.0.0 r-igraph@2.2.1 r-gprofiler2@0.2.4 r-enrichplot@1.30.3
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/adeschen/enrichViewNet
Licenses: Artistic License 2.0
Build system: r
Synopsis: From functional enrichment results to biological networks
Description:

This package enables the visualization of functional enrichment results as network graphs. First the package enables the visualization of enrichment results, in a format corresponding to the one generated by gprofiler2, as a customizable Cytoscape network. In those networks, both gene datasets (GO terms/pathways/protein complexes) and genes associated to the datasets are represented as nodes. While the edges connect each gene to its dataset(s). The package also provides the option to create enrichment maps from functional enrichment results. Enrichment maps enable the visualization of enriched terms into a network with edges connecting overlapping genes.

r-empiricalbrownsmethod 1.38.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/IlyaLab/CombiningDependentPvaluesUsingEBM.git
Licenses: Expat
Build system: r
Synopsis: Uses Brown's method to combine p-values from dependent tests
Description:

Combining P-values from multiple statistical tests is common in bioinformatics. However, this procedure is non-trivial for dependent P-values. This package implements an empirical adaptation of Brown’s Method (an extension of Fisher’s Method) for combining dependent P-values which is appropriate for highly correlated data sets found in high-throughput biological experiments.

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-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-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-eisar 1.22.1
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-limma@3.66.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-edger@4.8.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/fmicompbio/eisaR
Licenses: GPL 3
Build system: r
Synopsis: Exon-Intron Split Analysis (EISA) in R
Description:

Exon-intron split analysis (EISA) uses ordinary RNA-seq data to measure changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene expression. For details see Gaidatzis et al., Nat Biotechnol 2015. doi: 10.1038/nbt.3269. eisaR implements the major steps of EISA in R.

r-epicv2manifest 0.99.7
Propagated dependencies: r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EPICv2manifest
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina Infinium MethylationEPIC v2.0 extended manifest from Peters et al. 2024
Description:

This package provides a data.frame containing an extended probe manifest for the Illumina Infinium Methylation v2.0 Kit. Contains the complete manifest from the Illumina-provided EPIC-8v2-0_EA.csv, plus additional probewise information described in Peters et al. (2024).

r-ecolicdf 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/ecolicdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: ecolicdf
Description:

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

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.

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-ecoli2probe 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/ecoli2probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type ecoli2
Description:

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was E\_coli\_2\_probe\_tab.

r-epicompare 1.14.0
Propagated dependencies: r-stringr@1.6.0 r-seqinfo@1.0.0 r-rtracklayer@1.70.0 r-rmarkdown@2.30 r-reshape2@1.4.5 r-plotly@4.11.0 r-iranges@2.44.0 r-htmltools@0.5.8.1 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-genomation@1.42.0 r-downloadthis@0.5.0 r-data-table@1.17.8 r-chipseeker@1.46.1 r-biocgenerics@0.56.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/neurogenomics/EpiCompare
Licenses: GPL 3
Build system: r
Synopsis: Comparison, Benchmarking & QC of Epigenomic Datasets
Description:

EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. The package outputs an HTML report consisting of three sections: (1. General metrics) Metrics on peaks (percentage of blacklisted and non-standard peaks, and peak widths) and fragments (duplication rate) of samples, (2. Peak overlap) Percentage and statistical significance of overlapping and non-overlapping peaks. Also includes upset plot and (3. Functional annotation) functional annotation (ChromHMM, ChIPseeker and enrichment analysis) of peaks. Also includes peak enrichment around TSS.

r-epidecoder 1.18.0
Propagated dependencies: r-rtracklayer@1.70.0 r-rstatix@0.7.3 r-iranges@2.44.0 r-ggpubr@0.6.2 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-envstats@3.1.0 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/kandarpRJ/epidecodeR
Licenses: GPL 3
Build system: r
Synopsis: epidecodeR: a functional exploration tool for epigenetic and epitranscriptomic regulation
Description:

epidecodeR is a package capable of analysing impact of degree of DNA/RNA epigenetic chemical modifications on dysregulation of genes or proteins. This package integrates chemical modification data generated from a host of epigenomic or epitranscriptomic techniques such as ChIP-seq, ATAC-seq, m6A-seq, etc. and dysregulated gene lists in the form of differential gene expression, ribosome occupancy or differential protein translation and identify impact of dysregulation of genes caused due to varying degrees of chemical modifications associated with the genes. epidecodeR generates cumulative distribution function (CDF) plots showing shifts in trend of overall log2FC between genes divided into groups based on the degree of modification associated with the genes. The tool also tests for significance of difference in log2FC between groups of genes.

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-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-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-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-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-edge 2.42.0
Propagated dependencies: r-sva@3.58.0 r-qvalue@2.42.0 r-mass@7.3-65 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/jdstorey/edge
Licenses: Expat
Build system: r
Synopsis: Extraction of Differential Gene Expression
Description:

The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and generalized likelihood ratio tests (equivalent to F-tests and t-tests) are implemented for general study designs. Special functions are available to facilitate the analysis of common study designs, including time course experiments. Other packages such as sva and qvalue are integrated in edge to provide a wide range of tools for gene expression analysis.

r-ecoliprobe 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/ecoliprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type ecoli
Description:

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was E\_coli\_probe\_tab.

r-experimentsubset 1.20.0
Propagated dependencies: r-treesummarizedexperiment@2.18.0 r-summarizedexperiment@1.40.0 r-spatialexperiment@1.20.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-matrix@1.7-4
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/ExperimentSubset
Licenses: Expat
Build system: r
Synopsis: Manages subsets of data with Bioconductor Experiment objects
Description:

Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for one or more matrix-like assays along with the associated row and column data. Often only a subset of the original data is needed for down-stream analysis. For example, filtering out poor quality samples will require excluding some columns before analysis. The ExperimentSubset object is a container to efficiently manage different subsets of the same data without having to make separate objects for each new subset.

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Total results: 68658