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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-moe430bcdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/moe430bcdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: moe430bcdf
Description:

This package provides a package containing an environment representing the MOE430B.CDF file.

r-methylclock 1.16.0
Propagated dependencies: r-tidyverse@2.0.0 r-tidyr@1.3.1 r-tibble@3.3.0 r-rpmm@1.25 r-rcpp@1.1.0 r-quadprog@1.5-8 r-preprocesscore@1.72.0 r-planet@1.18.0 r-performanceanalytics@2.0.8 r-minfi@1.56.0 r-methylclockdata@1.18.0 r-impute@1.84.0 r-gridextra@2.3 r-ggpubr@0.6.2 r-ggpmisc@0.6.2 r-ggplot2@4.0.1 r-experimenthub@3.0.0 r-dynamictreecut@1.63-1 r-dplyr@1.1.4 r-devtools@2.4.6 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/isglobal-brge/methylclock
Licenses: Expat
Build system: r
Synopsis: Methylclock - DNA methylation-based clocks
Description:

This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath's clock, Hannum's clock, BNN, Horvath's skin+blood clock, PedBE clock and Wu's clock. Gestational DNAm age : Knight's clock, Bohlin's clock, Mayne's clock and Lee's clocks. Biological DNAm clocks : Levine's clock and Telomere Length's clock.

r-mafdb-exac-r1-0-grch38 3.10.0
Propagated dependencies: r-s4vectors@0.48.0 r-iranges@2.44.0 r-genomicscores@2.22.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MafDb.ExAC.r1.0.GRCh38
Licenses: Artistic License 2.0
Build system: r
Synopsis: Minor allele frequency data from ExAC release 1.0 for GRCh38
Description:

Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0) for the human genome version GRCh38.

r-mirnatap-db 0.99.10
Propagated dependencies: r-rsqlite@2.4.4 r-mirnatap@1.44.0 r-dbi@1.2.3 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/miRNAtap.db
Licenses: GPL 2
Build system: r
Synopsis: Data for miRNAtap
Description:

This package holds the database for miRNAtap.

r-multihiccompare 1.28.0
Propagated dependencies: r-qqman@0.1.9 r-pheatmap@1.0.13 r-pbapply@1.7-4 r-hiccompare@1.32.0 r-genomicranges@1.62.0 r-genomeinfodbdata@1.2.15 r-genomeinfodb@1.46.0 r-edger@4.8.0 r-dplyr@1.1.4 r-data-table@1.17.8 r-biocparallel@1.44.0 r-aggregation@1.0.1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/dozmorovlab/multiHiCcompare
Licenses: Expat
Build system: r
Synopsis: Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available
Description:

multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner.

r-michip 1.64.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MiChip
Licenses: GPL 2+
Build system: r
Synopsis: MiChip Parsing and Summarizing Functions
Description:

This package takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by otherBioConductor packages.

r-microbiomeprofiler 1.16.0
Propagated dependencies: r-yulab-utils@0.2.1 r-shinywidgets@0.9.0 r-shinycustomloader@0.9.0 r-shiny@1.11.1 r-magrittr@2.0.4 r-htmltools@0.5.8.1 r-gson@0.1.0 r-golem@0.5.1 r-ggplot2@4.0.1 r-enrichplot@1.30.3 r-dt@0.34.0 r-config@0.3.2 r-clusterprofiler@4.18.2
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/YuLab-SMU/MicrobiomeProfiler/
Licenses: GPL 2
Build system: r
Synopsis: An R/shiny package for microbiome functional enrichment analysis
Description:

This is an R/shiny package to perform functional enrichment analysis for microbiome data. This package was based on clusterProfiler. Moreover, MicrobiomeProfiler support KEGG enrichment analysis, COG enrichment analysis, Microbe-Disease association enrichment analysis, Metabo-Pathway analysis.

r-mariner 1.10.2
Propagated dependencies: r-summarizedexperiment@1.40.0 r-strawr@0.0.92 r-s4vectors@0.48.0 r-rlang@1.1.6 r-rhdf5@2.54.0 r-rcolorbrewer@1.1-3 r-purrr@1.2.0 r-progress@1.2.3 r-plotgardener@1.16.0 r-magrittr@2.0.4 r-iranges@2.44.0 r-interactionset@1.38.0 r-hdf5array@1.38.0 r-glue@1.8.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-dplyr@1.1.4 r-delayedarray@0.36.0 r-dbscan@1.2.3 r-data-table@1.17.8 r-colourvalues@0.3.11 r-biocparallel@1.44.0 r-biocmanager@1.30.27 r-biocgenerics@0.56.0 r-assertthat@0.2.1 r-abind@1.4-8
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://ericscottdavis.com/mariner/
Licenses: Expat
Build system: r
Synopsis: Mariner: Explore the Hi-Cs
Description:

This package provides tools for manipulating paired ranges and working with Hi-C data in R. Functionality includes manipulating/merging paired regions, generating paired ranges, extracting/aggregating interactions from `.hic` files, and visualizing the results. Designed for compatibility with plotgardener for visualization.

r-mogene11sttranscriptcluster-db 8.8.0
Propagated dependencies: r-org-mm-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mogene11sttranscriptcluster.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix mogene11 annotation data (chip mogene11sttranscriptcluster)
Description:

Affymetrix mogene11 annotation data (chip mogene11sttranscriptcluster) assembled using data from public repositories.

r-msstatsqc 2.28.0
Propagated dependencies: r-qcmetrics@1.48.0 r-plotly@4.11.0 r-msnbase@2.36.0 r-ggplot2@4.0.1 r-ggextra@0.11.0 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://msstats.org/msstatsqc
Licenses: FSDG-compatible
Build system: r
Synopsis: Longitudinal system suitability monitoring and quality control for proteomic experiments
Description:

MSstatsQC is an R package which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments.

r-mantelcorr 1.80.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MantelCorr
Licenses: GPL 2+
Build system: r
Synopsis: Compute Mantel Cluster Correlations
Description:

Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data).

r-mapredictdsc 1.48.0
Propagated dependencies: r-rocr@1.0-11 r-roc@1.86.0 r-mass@7.3-65 r-lungcanceracvssccgeo@1.46.0 r-limma@3.66.0 r-hgu133plus2-db@3.13.0 r-gcrma@2.82.0 r-e1071@1.7-16 r-class@7.3-23 r-caret@7.0-1 r-annotationdbi@1.72.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://bioinformaticsprb.med.wayne.edu/maPredictDSC
Licenses: GPL 2
Build system: r
Synopsis: Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Diagnostic Signature Challenge
Description:

This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types.

r-mbttest 1.38.0
Propagated dependencies: r-gtools@3.9.5 r-gplots@3.2.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MBttest
Licenses: GPL 3
Build system: r
Synopsis: Multiple Beta t-Tests
Description:

MBttest method was developed from beta t-test method of Baggerly et al(2003). Compared to baySeq (Hard castle and Kelly 2010), DESeq (Anders and Huber 2010) and exact test (Robinson and Smyth 2007, 2008) and the GLM of McCarthy et al(2012), MBttest is of high work efficiency,that is, it has high power, high conservativeness of FDR estimation and high stability. MBttest is suit- able to transcriptomic data, tag data, SAGE data (count data) from small samples or a few replicate libraries. It can be used to identify genes, mRNA isoforms or tags differentially expressed between two conditions.

r-mirsponger 2.14.1
Propagated dependencies: r-survival@3.8-3 r-sponge@1.32.0 r-reactomepa@1.54.0 r-rcpp@1.1.0 r-rcolorbrewer@1.1-3 r-org-hs-eg-db@3.22.0 r-mcl@1.0 r-igraph@2.2.1 r-foreach@1.5.2 r-dose@4.4.0 r-doparallel@1.0.17 r-corpcor@1.6.10 r-clusterprofiler@4.18.2
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: <https://github.com/zhangjunpeng411/miRspongeR>
Licenses: GPL 3
Build system: r
Synopsis: Identification and analysis of miRNA sponge regulation
Description:

This package provides several functions to explore miRNA sponge (also called ceRNA or miRNA decoy) regulation from putative miRNA-target interactions or/and transcriptomics data (including bulk, single-cell and spatial gene expression data). It provides eight popular methods for identifying miRNA sponge interactions, and an integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of miRNA sponge modules, and conduct survival analysis of miRNA sponge modules. By using a sample control variable strategy, it provides a function to infer sample-specific miRNA sponge interactions. In terms of sample-specific miRNA sponge interactions, it implements three similarity methods to construct sample-sample correlation network.

r-martini 1.30.0
Propagated dependencies: r-snpstats@1.60.0 r-rcppeigen@0.3.4.0.2 r-rcpp@1.1.0 r-memoise@2.0.1 r-matrix@1.7-4 r-igraph@2.2.1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/hclimente/martini
Licenses: GPL 3
Build system: r
Synopsis: GWAS Incorporating Networks
Description:

martini deals with the low power inherent to GWAS studies by using prior knowledge represented as a network. SNPs are the vertices of the network, and the edges represent biological relationships between them (genomic adjacency, belonging to the same gene, physical interaction between protein products). The network is scanned using SConES, which looks for groups of SNPs maximally associated with the phenotype, that form a close subnetwork.

r-mouse430a2-db 3.13.0
Propagated dependencies: r-org-mm-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mouse430a2.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix Mouse430A_2 Array annotation data (chip mouse430a2)
Description:

Affymetrix Affymetrix Mouse430A_2 Array annotation data (chip mouse430a2) assembled using data from public repositories.

r-mouseagingdata 1.6.0
Propagated dependencies: r-singlecellexperiment@1.32.0 r-experimenthub@3.0.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/ccb-hms/MouseAgingData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Multi-omics data access for studies investigating the effects of aging
Description:

The MouseAgingData package provides analysis-ready data resources from different studies focused on aging and rejuvenation in mice. The package currently provides two 10x Genomics single-cell RNA-seq datasets. The first study profiled the aging mouse brain measured across 37,089 cells (Ximerakis et al., 2019). The second study investigated parabiosis by profiling a total of 105,329 cells (Ximerakis & Holton et al., 2023). The datasets are provided as SingleCellExperiment objects and provide raw UMI counts and cell metadata.

r-mafdb-topmed-freeze5-hg19 3.10.0
Propagated dependencies: r-s4vectors@0.48.0 r-iranges@2.44.0 r-genomicscores@2.22.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MafDb.TOPMed.freeze5.hg19
Licenses: Artistic License 2.0
Build system: r
Synopsis: Minor allele frequency data from TOPMed for hg19
Description:

Store minor allele frequency data from NHLBI TOPMed for the human genome version hg19.

r-mirna20cdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mirna20cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: mirna20cdf
Description:

This package provides a package containing an environment representing the miRNA-2_0.cdf file.

r-macsr 1.18.0
Propagated dependencies: r-s4vectors@0.48.0 r-reticulate@1.44.1 r-experimenthub@3.0.0 r-basilisk@1.22.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MACSr
Licenses: Modified BSD
Build system: r
Synopsis: MACS: Model-based Analysis for ChIP-Seq
Description:

The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites. This package is an R wrapper of the lastest MACS3.

r-msdatahub 1.10.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://rformassspectrometry.github.io/MsDataHub
Licenses: Artistic License 2.0
Build system: r
Synopsis: Mass Spectrometry Data on ExperimentHub
Description:

The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments.

r-mcbiclust 1.34.0
Propagated dependencies: r-wgcna@1.73 r-scales@1.4.0 r-org-hs-eg-db@3.22.0 r-go-db@3.22.0 r-ggplot2@4.0.1 r-ggally@2.4.0 r-cluster@2.1.8.1 r-biocparallel@1.44.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MCbiclust
Licenses: GPL 2
Build system: r
Synopsis: Massive correlating biclusters for gene expression data and associated methods
Description:

Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

r-microbiomedatasets 1.18.0
Propagated dependencies: r-treesummarizedexperiment@2.18.0 r-summarizedexperiment@1.40.0 r-multiassayexperiment@1.36.1 r-experimenthub@3.0.0 r-biostrings@2.78.0 r-biocgenerics@0.56.0 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/microbiomeDataSets
Licenses: CC0
Build system: r
Synopsis: Experiment Hub based microbiome datasets
Description:

microbiomeDataSets is a collection of microbiome datasets loaded from Bioconductor'S ExperimentHub infrastructure. The datasets serve as reference for workflows and vignettes published adjacent to the microbiome analysis tools on Bioconductor. Additional datasets can be added overtime and additions from authors are welcome.

r-methylsig 1.22.0
Propagated dependencies: r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-dss@2.58.0 r-delayedmatrixstats@1.32.0 r-delayedarray@0.36.0 r-bsseq@1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/methylSig
Licenses: GPL 3
Build system: r
Synopsis: MethylSig: Differential Methylation Testing for WGBS and RRBS Data
Description:

MethylSig is a package for testing for differentially methylated cytosines (DMCs) or regions (DMRs) in whole-genome bisulfite sequencing (WGBS) or reduced representation bisulfite sequencing (RRBS) experiments. MethylSig uses a beta binomial model to test for significant differences between groups of samples. Several options exist for either site-specific or sliding window tests, and variance estimation.

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