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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-mai 1.16.0
Propagated dependencies: r-tidyverse@2.0.0 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-pcamethods@2.2.0 r-missforest@1.6.1 r-future-apply@1.20.0 r-future@1.68.0 r-foreach@1.5.2 r-e1071@1.7-16 r-doparallel@1.0.17 r-caret@7.0-1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/KechrisLab/MAI
Licenses: GPL 3
Synopsis: Mechanism-Aware Imputation
Description:

This package provides a two-step approach to imputing missing data in metabolomics. Step 1 uses a random forest classifier to classify missing values as either Missing Completely at Random/Missing At Random (MCAR/MAR) or Missing Not At Random (MNAR). MCAR/MAR are combined because it is often difficult to distinguish these two missing types in metabolomics data. Step 2 imputes the missing values based on the classified missing mechanisms, using the appropriate imputation algorithms. Imputation algorithms tested and available for MCAR/MAR include Bayesian Principal Component Analysis (BPCA), Multiple Imputation No-Skip K-Nearest Neighbors (Multi_nsKNN), and Random Forest. Imputation algorithms tested and available for MNAR include nsKNN and a single imputation approach for imputation of metabolites where left-censoring is present.

r-msbackendmassbank 1.18.0
Propagated dependencies: r-spectra@1.20.0 r-s4vectors@0.48.0 r-protgenerics@1.42.0 r-mscoreutils@1.21.0 r-iranges@2.44.0 r-dbi@1.2.3 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/RforMassSpectrometry/MsBackendMassbank
Licenses: Artistic License 2.0
Synopsis: Mass Spectrometry Data Backend for MassBank record Files
Description:

Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files. Different backends are available that allow handling of data in plain MassBank text file format or allow also to interact directly with MassBank SQL databases. Objects from this package are supposed to be used with the Spectra Bioconductor package. This package thus adds MassBank support to the Spectra package.

r-mpranalyze 1.28.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-progress@1.2.3 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/YosefLab/MPRAnalyze
Licenses: GPL 3
Synopsis: Statistical Analysis of MPRA data
Description:

MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quantification of enhancer activity, classification of active enhancers and comparative analyses of enhancer activity between conditions. MPRAnalyze construct a nested pair of generalized linear models (GLMs) to relate the DNA and RNA observations, easily adjustable to various experimental designs and conditions, and provides a set of rigorous statistical testig schemes.

r-meat 1.22.0
Propagated dependencies: r-watermelon@2.16.0 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-rpmm@1.25 r-minfi@1.56.0 r-impute@1.84.0 r-glmnet@4.1-10 r-dynamictreecut@1.63-1 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/sarah-voisin/MEAT
Licenses: Expat
Synopsis: Muscle Epigenetic Age Test
Description:

This package estimates epigenetic age in skeletal muscle, using DNA methylation data generated with the Illumina Infinium technology (HM27, HM450 and HMEPIC).

r-muspadata 1.2.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/peicai/muSpaData
Licenses: Expat
Synopsis: Multi-sample multi-group spatially resolved transcriptomic data
Description:

Data package containing a multi-sample multi-group spatial dataset in SpatialExperiment Bioconductor object format.

r-mmagilentdesign026655-db 3.2.3
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/MmAgilentDesign026655.db
Licenses: Artistic License 2.0
Synopsis: Agilent Chips that use Agilent design number 026655 annotation data (chip MmAgilentDesign026655)
Description:

Agilent Chips that use Agilent design number 026655 annotation data (chip MmAgilentDesign026655) assembled using data from public repositories.

r-methped 1.38.0
Propagated dependencies: r-randomforest@4.7-1.2 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MethPed
Licenses: GPL 2
Synopsis: DNA methylation classifier tool for the identification of pediatric brain tumor subtypes
Description:

Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. For this aim, we developed a diagnostic classifier based on DNA methylation profiles. We offer MethPed as an easy-to-use toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. The current version of MethPed can classify the following tumor diagnoses/subgroups: Diffuse Intrinsic Pontine Glioma (DIPG), Ependymoma, Embryonal tumors with multilayered rosettes (ETMR), Glioblastoma (GBM), Medulloblastoma (MB) - Group 3 (MB_Gr3), Group 4 (MB_Gr3), Group WNT (MB_WNT), Group SHH (MB_SHH) and Pilocytic Astrocytoma (PiloAstro).

r-mu19ksubccdf 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/mu19ksubccdf
Licenses: LGPL 2.0+
Synopsis: mu19ksubccdf
Description:

This package provides a package containing an environment representing the Mu19KsubC.CDF file.

r-methylseqdata 1.20.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rhdf5@2.54.0 r-iranges@2.44.0 r-hdf5array@1.38.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MethylSeqData
Licenses: CC0
Synopsis: Collection of Public DNA Methylation Sequencing Datasets
Description:

Base-level (i.e. cytosine-level) counts for a collection of public bisulfite-seq datasets (e.g., WGBS and RRBS), provided as SummarizedExperiment objects with sample- and base-level metadata.

r-mirnatarget 1.48.0
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/miRNATarget
Licenses: GPL 2+ GPL 3+
Synopsis: gene target tabale of miRNA for human/mouse used for MiRaGE package
Description:

gene target tabale of miRNA for human/mouse used for MiRaGE package.

r-mgug4122a-db 3.2.3
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/mgug4122a.db
Licenses: Artistic License 2.0
Synopsis: Agilent "Mouse Genome, Whole" annotation data (chip mgug4122a)
Description:

Agilent "Mouse Genome, Whole" annotation data (chip mgug4122a) assembled using data from public repositories.

r-mcseadata 1.30.0
Propagated dependencies: r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mCSEAdata
Licenses: GPL 2
Synopsis: Data package for mCSEA package
Description:

Data objects necessary to some mCSEA package functions. There are also example data objects to illustrate mCSEA package functionality.

r-methylgsa 1.28.0
Propagated dependencies: r-stringr@1.6.0 r-shiny@1.11.1 r-robustrankaggreg@1.2.1 r-reactome-db@1.94.0 r-org-hs-eg-db@3.22.0 r-missmethyl@1.44.0 r-illuminahumanmethylationepicanno-ilm10b4-hg19@0.6.0 r-illuminahumanmethylation450kanno-ilmn12-hg19@0.6.1 r-go-db@3.22.0 r-ggplot2@4.0.1 r-clusterprofiler@4.18.2 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://github.com/reese3928/methylGSA
Licenses: GPL 2
Synopsis: Gene Set Analysis Using the Outcome of Differential Methylation
Description:

The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as a covariate. methylRRA adjusts multiple p-values of each gene by Robust Rank Aggregation. For more detailed help information, please see the vignette.

r-mbamethyl 1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MBAmethyl
Licenses: Artistic License 2.0
Synopsis: Model-based analysis of DNA methylation data
Description:

This package provides a function for reconstructing DNA methylation values from raw measurements. It iteratively implements the group fused lars to smooth related-by-location methylation values and the constrained least squares to remove probe affinity effect across multiple sequences.

r-mirit 1.6.1
Propagated dependencies: r-rlang@1.1.6 r-rgraphviz@2.54.0 r-rcpp@1.1.0 r-multiassayexperiment@1.36.1 r-limma@3.66.0 r-httr@1.4.7 r-graphite@1.56.0 r-graph@1.88.0 r-ggpubr@0.6.2 r-ggplot2@4.0.1 r-geneset@0.2.7 r-genekitr@1.2.8 r-fgsea@1.36.0 r-edger@4.8.0 r-deseq2@1.50.2 r-biocparallel@1.44.0 r-biocfilecache@3.0.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/jacopo-ronchi/MIRit
Licenses: GPL 3+
Synopsis: Integrate microRNA and gene expression to decipher pathway complexity
Description:

MIRit is an R package that provides several methods for investigating the relationships between miRNAs and genes in different biological conditions. In particular, MIRit allows to explore the functions of dysregulated miRNAs, and makes it possible to identify miRNA-gene regulatory axes that control biological pathways, thus enabling the users to unveil the complexity of miRNA biology. MIRit is an all-in-one framework that aims to help researchers in all the central aspects of an integrative miRNA-mRNA analyses, from differential expression analysis to network characterization.

r-methylscaper 1.18.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-shinyjs@2.1.0 r-shinyfiles@0.9.3 r-shiny@1.11.1 r-seriation@1.5.8 r-seqinr@4.2-36 r-rfast@2.1.5.2 r-pwalign@1.6.0 r-data-table@1.17.8 r-biostrings@2.78.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/rhondabacher/methylscaper/
Licenses: GPL 2
Synopsis: Visualization of Methylation Data
Description:

methylscaper is an R package for processing and visualizing data jointly profiling methylation and chromatin accessibility (MAPit, NOMe-seq, scNMT-seq, nanoNOMe, etc.). The package supports both single-cell and single-molecule data, and a common interface for jointly visualizing both data types through the generation of ordered representational methylation-state matrices. The Shiny app allows for an interactive seriation process of refinement and re-weighting that optimally orders the cells or DNA molecules to discover methylation patterns and nucleosome positioning.

r-msbackendrawfilereader 1.16.0
Propagated dependencies: r-spectra@1.20.0 r-s4vectors@0.48.0 r-rawrr@1.18.0 r-protgenerics@1.42.0 r-mscoreutils@1.21.0 r-iranges@2.44.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/fgcz/MsBackendRawFileReader
Licenses: GPL 3
Synopsis: Mass Spectrometry Backend for Reading Thermo Fisher Scientific raw Files
Description:

implements a MsBackend for the Spectra package using Thermo Fisher Scientific's NewRawFileReader .Net libraries. The package is generalizing the functionality introduced by the rawrr package Methods defined in this package are supposed to extend the Spectra Bioconductor package.

r-mira 1.32.0
Propagated dependencies: r-s4vectors@0.48.0 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-data-table@1.17.8 r-bsseq@1.46.0 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://databio.org/mira
Licenses: GPL 3
Synopsis: Methylation-Based Inference of Regulatory Activity
Description:

DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for a given region set with shared biological annotation. Using this profile, MIRA infers and scores the collective regulatory activity for the region set. MIRA facilitates regulatory analysis in situations where classical regulatory assays would be difficult and allows public sources of region sets to be leveraged for novel insight into the regulatory state of DNA methylation datasets.

r-mirage 1.52.0
Propagated dependencies: r-s4vectors@0.48.0 r-biocmanager@1.30.27 r-biocgenerics@0.56.0 r-biobase@2.70.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MiRaGE
Licenses: GPL 2+ GPL 3+
Synopsis: MiRNA Ranking by Gene Expression
Description:

The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile.

r-mgu74av2-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/mgu74av2.db
Licenses: Artistic License 2.0
Synopsis: Affymetrix Affymetrix MG_U74Av2 Array annotation data (chip mgu74av2)
Description:

Affymetrix Affymetrix MG_U74Av2 Array annotation data (chip mgu74av2) assembled using data from public repositories.

r-mpra 1.32.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-statmod@1.5.1 r-scales@1.4.0 r-s4vectors@0.48.0 r-limma@3.66.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/hansenlab/mpra
Licenses: Artistic License 2.0
Synopsis: Analyze massively parallel reporter assays
Description:

This package provides tools for data management, count preprocessing, and differential analysis in massively parallel report assays (MPRA).

r-mirbaseversions-db 1.1.0
Propagated dependencies: r-rsqlite@2.4.4 r-gtools@3.9.5 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/miRBaseVersions.db
Licenses: Artistic License 2.0
Synopsis: Collection of mature miRNA names of 22 different miRBase release versions
Description:

Annotation package containing all available miRNA names from 22 versions (data from http://www.mirbase.org/).

r-mirlab 1.40.0
Propagated dependencies: r-tcgabiolinks@2.38.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-rcurl@1.98-1.17 r-pcalg@2.7-12 r-org-hs-eg-db@3.22.0 r-limma@3.66.0 r-invariantcausalprediction@0.8 r-impute@1.84.0 r-httr@1.4.7 r-hmisc@5.2-4 r-gplots@3.2.0 r-gostats@2.76.0 r-glmnet@4.1-10 r-entropy@1.3.2 r-energy@1.7-12 r-dplyr@1.1.4 r-ctc@1.84.0 r-category@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/pvvhoang/miRLAB
Licenses: FSDG-compatible
Synopsis: Dry lab for exploring miRNA-mRNA relationships
Description:

Provide tools exploring miRNA-mRNA relationships, including popular miRNA target prediction methods, ensemble methods that integrate individual methods, functions to get data from online resources, functions to validate the results, and functions to conduct enrichment analyses.

r-msprep 1.19.0
Propagated dependencies: r-vim@6.2.6 r-tidyr@1.3.1 r-tibble@3.3.0 r-sva@3.58.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-s4vectors@0.48.0 r-rlang@1.1.6 r-preprocesscore@1.72.0 r-pcamethods@2.2.0 r-missforest@1.6.1 r-magrittr@2.0.4 r-dplyr@1.1.4 r-crmn@0.0.21
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/KechrisLab/MSPrep
Licenses: GPL 3
Synopsis: Package for Summarizing, Filtering, Imputing, and Normalizing Metabolomics Data
Description:

Package performs summarization of replicates, filtering by frequency, several different options for imputing missing data, and a variety of options for transforming, batch correcting, and normalizing data.

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Total results: 68249