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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.

If you'd like to join our channel webring send a patch to ~whereiseveryone/toys@lists.sr.ht adding your channel as an entry in channels.scm.


r-mirnatap-db 0.99.10
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-multiwgcnadata 1.8.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/multiWGCNAdata
Licenses: Artistic License 2.0
Build system: r
Synopsis: Data Package for multiWGCNA
Description:

Stores expression profiling data from experiments compatible with the multiWGCNA R package. This includes human postmortem microarray data from patients and controls (GSE28521), astrocyte Ribotag RNA-seq data from EAE and wildtype mice (GSE100329), and mouse RNA-seq data from tau pathology (rTg4510) and wildtype control mice (GSE125957). These data can be accessed using the ExperimentHub workflow (see multiWGCNA vignettes).

r-mouse4302frmavecs 1.5.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mouse4302frmavecs
Licenses: GPL 2+
Build system: r
Synopsis: Vectors used by frma for microarrays of type mouse4302
Description:

This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.

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+
Build system: r
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-measurementerror-cor 1.82.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MeasurementError.cor
Licenses: LGPL 2.0+
Build system: r
Synopsis: Measurement Error model estimate for correlation coefficient
Description:

Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation.

r-mdts 1.30.0
Propagated dependencies: r-stringr@1.6.0 r-rsamtools@2.26.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicalignments@1.46.0 r-dnacopy@1.84.0 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MDTS
Licenses: Artistic License 2.0
Build system: r
Synopsis: Detection of de novo deletion in targeted sequencing trios
Description:

This package provides a package for the detection of de novo copy number deletions in targeted sequencing of trios with high sensitivity and positive predictive value.

r-mafdb-1kgenomes-phase1-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.1Kgenomes.phase1.GRCh38
Licenses: Artistic License 2.0
Build system: r
Synopsis: Minor allele frequency data from 1000 Genomes Phase 1 for GRCh38
Description:

Store minor allele frequency data from the Phase 1 of the 1000 Genomes Project for the human genome version GRCh38.

r-m6aboost 1.16.0
Propagated dependencies: r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-experimenthub@3.0.0 r-dplyr@1.1.4 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-adabag@5.1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/ZarnackGroup/m6Aboost
Licenses: Artistic License 2.0
Build system: r
Synopsis: m6Aboost
Description:

This package can help user to run the m6Aboost model on their own miCLIP2 data. The package includes functions to assign the read counts and get the features to run the m6Aboost model. The miCLIP2 data should be stored in a GRanges object. More details can be found in the vignette.

r-msbackendmsp 1.14.0
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-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/RforMassSpectrometry/MsBackendMsp
Licenses: Artistic License 2.0
Build system: r
Synopsis: Mass Spectrometry Data Backend for NIST msp Files
Description:

Mass spectrometry (MS) data backend supporting import and handling of MS/MS spectra from NIST MSP Format (msp) files. Import of data from files with different MSP *flavours* is supported. Objects from this package add support for MSP files to Bioconductor's Spectra package. This package is thus not supposed to be used without the Spectra package that provides a complete infrastructure for MS data handling.

r-mta10probeset-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/mta10probeset.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix mta10 annotation data (chip mta10probeset)
Description:

Affymetrix mta10 annotation data (chip mta10probeset) assembled using data from public repositories.

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.

r-mu19ksuba-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/mu19ksuba.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix Mu19KsubA Array annotation data (chip mu19ksuba)
Description:

Affymetrix Affymetrix Mu19KsubA Array annotation data (chip mu19ksuba) assembled using data from public repositories.

r-metacca 1.38.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://doi.org/10.1093/bioinformatics/btw052
Licenses: Expat
Build system: r
Synopsis: Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
Description:

metaCCA performs multivariate analysis of a single or multiple GWAS based on univariate regression coefficients. It allows multivariate representation of both phenotype and genotype. metaCCA extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness.

r-metaboliteidmapping 1.0.0
Propagated dependencies: r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/yigbt/metaboliteIDmapping
Licenses: GPL 3
Build system: r
Synopsis: Mapping of Metabolite IDs from Different Sources
Description:

The package provides a comprehensive mapping table of nine different Metabolite ID formats and their common name. The data has been collected and merged from four publicly available source, including HMDB, Comptox Dashboard, ChEBI, and the graphite Bioconductor R package.

r-moda 1.36.0
Propagated dependencies: r-wgcna@1.73 r-rcolorbrewer@1.1-3 r-igraph@2.2.1 r-dynamictreecut@1.63-1 r-cluster@2.1.8.1 r-amountain@1.36.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MODA
Licenses: GPL 2+
Build system: r
Synopsis: MODA: MOdule Differential Analysis for weighted gene co-expression network
Description:

MODA can be used to estimate and construct condition-specific gene co-expression networks, and identify differentially expressed subnetworks as conserved or condition specific modules which are potentially associated with relevant biological processes.

r-mosaicsexample 1.48.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://groups.google.com/group/mosaics_user_group
Licenses: GPL 2+
Build system: r
Synopsis: Example data for the mosaics package, which implements MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data for transcription factor binding and histone modification
Description:

Data for the mosaics package, consisting of (1) chromosome 22 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding and H3K4me3 modification in MCF7 cell line from ENCODE database (HG19) and (2) chromosome 21 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding, with mappability, GC content, and sequence ambiguity scores of human genome HG18.

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
Build system: r
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-moonlight2r 1.8.1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/ELELAB/Moonlight2R
Licenses: GPL 3
Build system: r
Synopsis: Identify oncogenes and tumor suppressor genes from omics data
Description:

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). We present an updated version of the R/bioconductor package called MoonlightR, namely Moonlight2R, which returns a list of candidate driver genes for specific cancer types on the basis of omics data integration. The Moonlight framework contains a primary layer where gene expression data and information about biological processes are integrated to predict genes called oncogenic mediators, divided into putative tumor suppressors and putative oncogenes. This is done through functional enrichment analyses, gene regulatory networks and upstream regulator analyses to score the importance of well-known biological processes with respect to the studied cancer type. By evaluating the effect of the oncogenic mediators on biological processes or through random forests, the primary layer predicts two putative roles for the oncogenic mediators: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As gene expression data alone is not enough to explain the deregulation of the genes, a second layer of evidence is needed. We have automated the integration of a secondary mutational layer through new functionalities in Moonlight2R. These functionalities analyze mutations in the cancer cohort and classifies these into driver and passenger mutations using the driver mutation prediction tool, CScape-somatic. Those oncogenic mediators with at least one driver mutation are retained as the driver genes. 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, Moonlight2R can be used to discover OCGs and TSGs in the same cancer type. This may for instance help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV). In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments. An additional mechanistic layer evaluates if there are mutations affecting the protein stability of the transcription factors (TFs) of the TSGs and OCGs, as that may have an effect on the expression of the genes.

r-mu6500subdcdf 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/mu6500subdcdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: mu6500subdcdf
Description:

This package provides a package containing an environment representing the Mu6500subD.CDF file.

r-metascope 1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MetaScope
Licenses: GPL 3+
Build system: r
Synopsis: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data
Description:

This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is in part an R translation of the PathoScope 2.0 pipeline.

r-memes 1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://snystrom.github.io/memes/
Licenses: Expat
Build system: r
Synopsis: motif matching, comparison, and de novo discovery using the MEME Suite
Description:

This package provides a seamless interface to the MEME Suite family of tools for motif analysis. memes provides data aware utilities for using GRanges objects as entrypoints to motif analysis, data structures for examining & editing motif lists, and novel data visualizations. memes functions and data structures are amenable to both base R and tidyverse workflows.

r-methped 1.38.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MethPed
Licenses: GPL 2
Build system: r
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-marker 1.0.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://diseasetranscriptomicslab.github.io/markeR/
Licenses: Artistic License 2.0
Build system: r
Synopsis: An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
Description:

markeR is an R package that provides a modular and extensible framework for the systematic evaluation of gene sets as phenotypic markers using transcriptomic data. The package is designed to support both quantitative analyses and visual exploration of gene set behaviour across experimental and clinical phenotypes. It implements multiple methods, including score-based and enrichment approaches, and also allows the exploration of expression behaviour of individual genes. In addition, users can assess the similarity of their own gene sets against established collections (e.g., those from MSigDB), facilitating biological interpretation.

r-mgu74bv2-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/mgu74bv2.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix MG_U74Bv2 Array annotation data (chip mgu74bv2)
Description:

Affymetrix Affymetrix MG_U74Bv2 Array annotation data (chip mgu74bv2) assembled using data from public repositories.

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Total results: 69112