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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.

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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-epinem 1.34.0
Propagated dependencies: r-rcolorbrewer@1.1-3 r-pcalg@2.7-12 r-mnem@1.26.0 r-minet@3.68.0 r-latticeextra@0.6-31 r-lattice@0.22-7 r-latex2exp@0.9.6 r-igraph@2.2.1 r-gtools@3.9.5 r-graph@1.88.0 r-e1071@1.7-16 r-boutroslab-plotting-general@7.1.5 r-boolnet@2.1.9
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/cbg-ethz/epiNEM/
Licenses: GPL 3
Build system: r
Synopsis: epiNEM
Description:

epiNEM is an extension of the original Nested Effects Models (NEM). EpiNEM is able to take into account double knockouts and infer more complex network signalling pathways. It is tailored towards large scale double knock-out screens.

r-ewce 1.18.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-singlecellexperiment@1.32.0 r-rnomni@1.0.1.2 r-reshape2@1.4.5 r-orthogene@1.16.1 r-matrix@1.7-4 r-limma@3.66.0 r-hgnchelper@0.8.15 r-ggplot2@4.0.1 r-ewcedata@1.18.0 r-dplyr@1.1.4 r-delayedarray@0.36.0 r-data-table@1.17.8 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/NathanSkene/EWCE
Licenses: GPL 3
Build system: r
Synopsis: Expression Weighted Celltype Enrichment
Description:

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-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-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-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-eupathdb 1.0.1
Propagated dependencies: r-genomicranges@1.62.0 r-genomeinfodbdata@1.2.15 r-biostrings@2.78.0 r-biocmanager@1.30.27 r-biobase@2.70.0 r-annotationhubdata@1.40.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/khughitt/EuPathDB
Licenses: Artistic License 2.0
Build system: r
Synopsis: Provides access to pathogen annotation resources available on EuPathDB databases
Description:

Brings together annotation resources from the various EuPathDB databases (PlasmoDB, ToxoDB, TriTrypDB, etc.) and makes them available in R using the AnnotationHub framework.

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-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-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-excluster 1.28.0
Propagated dependencies: r-rtracklayer@1.70.0 r-rsubread@2.24.0 r-matrixstats@1.5.0 r-iranges@2.44.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/ExCluster
Licenses: GPL 3
Build system: r
Synopsis: ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition
Description:

ExCluster flattens Ensembl and GENCODE GTF files into GFF files, which are used to count reads per non-overlapping exon bin from BAM files. This read counting is done using the function featureCounts from the package Rsubread. Library sizes are normalized across all biological replicates, and ExCluster then compares two different conditions to detect signifcantly differentially spliced genes. This process requires at least two independent biological repliates per condition, and ExCluster accepts only exactly two conditions at a time. ExCluster ultimately produces false discovery rates (FDRs) per gene, which are used to detect significance. Exon log2 fold change (log2FC) means and variances may be plotted for each significantly differentially spliced gene, which helps scientists develop hypothesis and target differential splicing events for RT-qPCR validation in the wet lab.

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-evaluomer 1.26.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-sparcl@1.0.4 r-rskc@2.4.2 r-reshape2@1.4.5 r-rdpack@2.6.4 r-randomforest@4.7-1.2 r-prabclus@2.3-4 r-plotrix@3.8-13 r-multiassayexperiment@1.36.1 r-mclust@6.1.2 r-matrixstats@1.5.0 r-mass@7.3-65 r-kableextra@1.4.0 r-ggplot2@4.0.1 r-ggdendro@0.2.0 r-fpc@2.2-13 r-flexmix@2.3-20 r-dplyr@1.1.4 r-dendextend@1.19.1 r-corrplot@0.95 r-cluster@2.1.8.1 r-class@7.3-23
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/neobernad/evaluomeR
Licenses: GPL 3
Build system: r
Synopsis: Evaluation of Bioinformatics Metrics
Description:

Evaluating the reliability of your own metrics and the measurements done on your own datasets by analysing the stability and goodness of the classifications of such metrics.

r-enmcb 1.22.0
Propagated dependencies: r-survivalsvm@0.0.6 r-survivalroc@1.0.3.1 r-survival@3.8-3 r-rms@8.1-0 r-mboost@2.9-11 r-matrix@1.7-4 r-igraph@2.2.1 r-glmnet@4.1-10 r-ggplot2@4.0.1 r-e1071@1.7-16 r-boot@1.3-32 r-biocfilecache@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EnMCB
Licenses: GPL 2
Build system: r
Synopsis: Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models
Description:

Creation of the correlated blocks using DNA methylation profiles. Machine learning models can be constructed to predict differentially methylated blocks and disease progression.

r-ecoli2cdf 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/ecoli2cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: ecoli2cdf
Description:

This package provides a package containing an environment representing the E_coli_2.cdf file.

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-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-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-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-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-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-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-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.

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