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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.

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r-mogene10sttranscriptcluster-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/mogene10sttranscriptcluster.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix mogene10 annotation data (chip mogene10sttranscriptcluster)
Description:

Affymetrix mogene10 annotation data (chip mogene10sttranscriptcluster) assembled using data from public repositories.

r-mogene11stprobeset-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/mogene11stprobeset.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix mogene11 annotation data (chip mogene11stprobeset)
Description:

Affymetrix mogene11 annotation data (chip mogene11stprobeset) assembled using data from public repositories.

r-multirnaflow 1.8.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/loubator/MultiRNAflow
Licenses: GPL 3 FSDG-compatible
Build system: r
Synopsis: An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions
Description:

Our R package MultiRNAflow provides an easy to use unified framework allowing to automatically make both unsupervised and supervised (DE) analysis for datasets with an arbitrary number of biological conditions and time points. In particular, our code makes a deep downstream analysis of DE information, e.g. identifying temporal patterns across biological conditions and DE genes which are specific to a biological condition for each time.

r-m3drop 1.36.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/tallulandrews/M3Drop
Licenses: FSDG-compatible
Build system: r
Synopsis: Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
Description:

This package fits a model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells. Also includes an method for calculating exact Pearson residuals in UMI-tagged data using a library-size aware negative binomial model.

r-mosbi 1.16.0
Propagated dependencies: r-xml2@1.5.0 r-rcppparallel@5.1.11-1 r-rcpp@1.1.0 r-rcolorbrewer@1.1-3 r-qubic@1.38.0 r-isa2@0.3.6 r-igraph@2.2.1 r-fabia@2.56.0 r-biclust@2.0.3.1 r-bh@1.87.0-1 r-akmbiclust@0.1.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mosbi
Licenses: FSDG-compatible
Build system: r
Synopsis: Molecular Signature identification using Biclustering
Description:

This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract bicluster communities from the similarity network, which can then be converted to ensemble biclusters. Additionally, MoSBi includes several network visualization methods to give an intuitive and scalable overview of the results. MoSBi comes with several biclustering algorithms, but can be easily extended to new biclustering algorithms.

r-moonlightr 1.36.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/ELELAB/MoonlightR
Licenses: GPL 3+
Build system: r
Synopsis: Identify oncogenes and tumor suppressor genes from omics data
Description:

Motivation: The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). Results: We present an R/bioconductor package called MoonlightR which returns a list of candidate driver genes for specific cancer types on the basis of TCGA expression data. The method first infers gene regulatory networks and then carries out a functional enrichment analysis (FEA) (implementing an upstream regulator analysis, URA) to score the importance of well-known biological processes with respect to the studied cancer type. Eventually, by means of random forests, MoonlightR predicts two specific roles for the candidate driver genes: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, MoonlightR can be used to discover OCGs and TSGs in the same cancer type. This may help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV) in breast cancer. In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments.

r-mastr 1.10.2
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://davislaboratory.github.io/mastR
Licenses: Expat
Build system: r
Synopsis: Markers Automated Screening Tool in R
Description:

mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from edgeR and limma differential expression (DE) analysis workflow. It also takes into account the background noise of tissue-specificity, which is often ignored by other marker generation tools. This package is particularly useful for the identification of group markers in various biological and medical applications, including cancer research and developmental biology.

r-mineica 1.49.0
Propagated dependencies: r-xtable@1.8-4 r-scales@1.4.0 r-rgraphviz@2.54.0 r-rcolorbrewer@1.1-3 r-plyr@1.8.9 r-mclust@6.1.2 r-marray@1.88.0 r-lumihumanall-db@1.22.0 r-lumi@2.62.0 r-jade@2.0-4 r-igraph@2.2.1 r-hmisc@5.2-4 r-gtools@3.9.5 r-graph@1.88.0 r-gostats@2.76.0 r-ggplot2@4.0.1 r-fpc@2.2-13 r-foreach@1.5.2 r-fastica@1.2-7 r-colorspace@2.1-2 r-cluster@2.1.8.1 r-biomart@2.66.0 r-biocgenerics@0.56.0 r-biobase@2.70.0 r-annotationdbi@1.72.0 r-annotate@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MineICA
Licenses: GPL 2
Build system: r
Synopsis: Analysis of an ICA decomposition obtained on genomics data
Description:

The goal of MineICA is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This Integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph.

r-mpedbarray-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/mpedbarray.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: FHCRC Nelson Lab mpedbarray Annotation Data (mpedbarray)
Description:

FHCRC Nelson Lab mpedbarray Annotation Data (mpedbarray) assembled using data from public repositories.

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-mogene20sttranscriptcluster-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/mogene20sttranscriptcluster.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix mogene20 annotation data (chip mogene20sttranscriptcluster)
Description:

Affymetrix mogene20 annotation data (chip mogene20sttranscriptcluster) assembled using data from public repositories.

r-metams 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/yguitton/metaMS
Licenses: GPL 2+
Build system: r
Synopsis: MS-based metabolomics annotation pipeline
Description:

MS-based metabolomics data processing and compound annotation pipeline.

r-mgu74ccdf 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/mgu74ccdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: mgu74ccdf
Description:

This package provides a package containing an environment representing the MG_U74C.cdf file.

r-masigpro 1.82.0
Propagated dependencies: r-venn@1.12 r-mclust@6.1.2 r-mass@7.3-65 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/maSigPro
Licenses: GPL 2+
Build system: r
Synopsis: Significant Gene Expression Profile Differences in Time Course Gene Expression Data
Description:

maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.

r-mtbls2 1.40.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://www.ebi.ac.uk/metabolights/MTBLS2
Licenses: CC0
Build system: r
Synopsis: MetaboLights MTBLS2: Comparative LC/MS-based profiling of silver nitrate-treated Arabidopsis thaliana leaves of wild-type and cyp79B2 cyp79B3 double knockout plants. Böttcher et al. (2004)
Description:

Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2'-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites.

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-multistateqtl 2.2.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/dunstone-a/multistateQTL
Licenses: GPL 3
Build system: r
Synopsis: Toolkit for the analysis of multi-state QTL data
Description:

This package provides a collection of tools for doing various analyses of multi-state QTL data, with a focus on visualization and interpretation. The package multistateQTL contains functions which can remove or impute missing data, identify significant associations, as well as categorise features into global, multi-state or unique. The analysis results are stored in a QTLExperiment object, which is based on the SummarisedExperiment framework.

r-microbiomeexplorer 1.20.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/microbiomeExplorer
Licenses: Expat
Build system: r
Synopsis: Microbiome Exploration App
Description:

The MicrobiomeExplorer R package is designed to facilitate the analysis and visualization of marker-gene survey feature data. It allows a user to perform and visualize typical microbiome analytical workflows either through the command line or an interactive Shiny application included with the package. In addition to applying common analytical workflows the application enables automated analysis report generation.

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
Build system: r
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-mgu74c-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/mgu74c.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix MG_U74C Array annotation data (chip mgu74c)
Description:

Affymetrix Affymetrix MG_U74C Array annotation data (chip mgu74c) assembled using data from public repositories.

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-methylcc 1.24.1
Propagated dependencies: r-s4vectors@0.48.0 r-quadprog@1.5-8 r-minfi@1.56.0 r-magrittr@2.0.4 r-iranges@2.44.0 r-illuminahumanmethylation450kmanifest@0.4.0 r-illuminahumanmethylation450kanno-ilmn12-hg19@0.6.1 r-genomicranges@1.62.0 r-genefilter@1.92.0 r-flowsorted-blood-450k@1.48.0 r-dplyr@1.1.4 r-bumphunter@1.52.0 r-bsseq@1.46.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/stephaniehicks/methylCC/
Licenses: GPL 3
Build system: r
Synopsis: Estimate the cell composition of whole blood in DNA methylation samples
Description:

This package provides a tool to estimate the cell composition of DNA methylation whole blood sample measured on any platform technology (microarray and sequencing).

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-metaseq 1.50.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/metaSeq
Licenses: Artistic License 2.0
Build system: r
Synopsis: Meta-analysis of RNA-Seq count data in multiple studies
Description:

The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method.

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Total results: 69112