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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-magrene 1.12.0
Propagated dependencies: r-biocparallel@1.42.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/almeidasilvaf/magrene
Licenses: GPL 3
Synopsis: Motif Analysis In Gene Regulatory Networks
Description:

magrene allows the identification and analysis of graph motifs in (duplicated) gene regulatory networks (GRNs), including lambda, V, PPI V, delta, and bifan motifs. GRNs can be tested for motif enrichment by comparing motif frequencies to a null distribution generated from degree-preserving simulated GRNs. Motif frequencies can be analyzed in the context of gene duplications to explore the impact of small-scale and whole-genome duplications on gene regulatory networks. Finally, users can calculate interaction similarity for gene pairs based on the Sorensen-Dice similarity index.

r-microbiomedasim 1.24.0
Propagated dependencies: r-tmvtnorm@1.6 r-phyloseq@1.52.0 r-pbapply@1.7-2 r-mvtnorm@1.3-3 r-metagenomeseq@1.50.0 r-matrix@1.7-3 r-mass@7.3-65 r-ggplot2@3.5.2 r-biobase@2.68.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/williazo/microbiomeDASim
Licenses: Expat
Synopsis: Microbiome Differential Abundance Simulation
Description:

This package provides a toolkit for simulating differential microbiome data designed for longitudinal analyses. Several functional forms may be specified for the mean trend. Observations are drawn from a multivariate normal model. The objective of this package is to be able to simulate data in order to accurately compare different longitudinal methods for differential abundance.

r-mi16cod-db 3.4.0
Propagated dependencies: r-org-mm-eg-db@3.21.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mi16cod.db
Licenses: Artistic License 2.0
Synopsis: Codelink Mouse Inflammation 16 Bioarray annotation data (chip mi16cod)
Description:

Codelink Mouse Inflammation 16 Bioarray annotation data (chip mi16cod) assembled using data from public repositories.

r-mouse4302probe 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mouse4302probe
Licenses: LGPL 2.0+
Synopsis: Probe sequence data for microarrays of type mouse4302
Description:

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mouse430\_2\_probe\_tab.

r-moe430aprobe 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/moe430aprobe
Licenses: LGPL 2.0+
Synopsis: Probe sequence data for microarrays of type moe430a
Description:

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MOE430A\_probe\_tab.

r-mait 1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MAIT
Licenses: GPL 2
Synopsis: Statistical Analysis of Metabolomic Data
Description:

The MAIT package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions.

r-myvariant 1.40.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/myvariant
Licenses: Artistic License 2.0
Synopsis: Accesses MyVariant.info variant query and annotation services
Description:

MyVariant.info is a comprehensive aggregation of variant annotation resources. myvariant is a wrapper for querying MyVariant.info services.

r-miaviz 1.18.0
Propagated dependencies: r-viridis@0.6.5 r-treesummarizedexperiment@2.16.1 r-tidytree@0.4.6 r-tidytext@0.4.2 r-tidyr@1.3.1 r-tidygraph@1.3.1 r-tibble@3.2.1 r-summarizedexperiment@1.38.1 r-singlecellexperiment@1.30.1 r-scater@1.36.0 r-scales@1.4.0 r-s4vectors@0.46.0 r-rlang@1.1.6 r-mia@1.16.0 r-ggtree@3.16.0 r-ggrepel@0.9.6 r-ggraph@2.2.1 r-ggplot2@3.5.2 r-ggnewscale@0.5.1 r-dplyr@1.1.4 r-dirichletmultinomial@1.50.0 r-delayedarray@0.34.1 r-biocparallel@1.42.0 r-biocgenerics@0.54.0 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/microbiome/miaViz
Licenses: Artistic License 2.0 FSDG-compatible
Synopsis: Microbiome Analysis Plotting and Visualization
Description:

The miaViz package implements functions to visualize TreeSummarizedExperiment objects especially in the context of microbiome analysis. Part of the mia family of R/Bioconductor packages.

r-mapredictdsc 1.48.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://bioinformaticsprb.med.wayne.edu/maPredictDSC
Licenses: GPL 2
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-mitology 1.2.0
Propagated dependencies: r-scales@1.4.0 r-reactomepa@1.52.0 r-org-hs-eg-db@3.21.0 r-magrittr@2.0.3 r-ggtree@3.16.0 r-ggplot2@3.5.2 r-complexheatmap@2.24.0 r-clusterprofiler@4.16.0 r-circlize@0.4.16 r-ape@5.8-1 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/CaluraLab/mitology
Licenses: AGPL 3
Synopsis: Study of mitochondrial activity from RNA-seq data
Description:

mitology allows to study the mitochondrial activity throught high-throughput RNA-seq data. It is based on a collection of genes whose proteins localize in to the mitochondria. From these, mitology provides a reorganization of the pathways related to mitochondria activity from Reactome and Gene Ontology. Further a ready-to-use implementation of MitoCarta3.0 pathways is included.

r-mcsurvdata 1.28.0
Propagated dependencies: r-experimenthub@2.16.0 r-biobase@2.68.0 r-annotationhub@3.16.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/adricaba/mcsurvdata
Licenses: FSDG-compatible
Synopsis: Meta cohort survival data
Description:

This package stores two merged expressionSet objects that contain the gene expression profile and clinical information of -a- six breast cancer cohorts and -b- four colorectal cancer cohorts. Breast cancer data are employed in the vignette of the hrunbiased package for survival analysis of gene signatures.

r-methped 1.38.0
Propagated dependencies: r-randomforest@4.7-1.2 r-biobase@2.68.0
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-metabcombiner 1.20.0
Propagated dependencies: r-tidyr@1.3.1 r-s4vectors@0.46.0 r-rlang@1.1.6 r-mgcv@1.9-3 r-matrixstats@1.5.0 r-dplyr@1.1.4 r-caret@7.0-1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/metabCombiner
Licenses: GPL 3
Synopsis: Method for Combining LC-MS Metabolomics Feature Measurements
Description:

This package aligns LC-HRMS metabolomics datasets acquired from biologically similar specimens analyzed under similar, but not necessarily identical, conditions. Peak-picked and simply aligned metabolomics feature tables (consisting of m/z, rt, and per-sample abundance measurements, plus optional identifiers & adduct annotations) are accepted as input. The package outputs a combined table of feature pair alignments, organized into groups of similar m/z, and ranked by a similarity score. Input tables are assumed to be acquired using similar (but not necessarily identical) analytical methods.

r-mina 1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mina
Licenses: GPL 2+ GPL 3+
Synopsis: Microbial community dIversity and Network Analysis
Description:

An increasing number of microbiome datasets have been generated and analyzed with the help of rapidly developing sequencing technologies. At present, analysis of taxonomic profiling data is mainly conducted using composition-based methods, which ignores interactions between community members. Besides this, a lack of efficient ways to compare microbial interaction networks limited the study of community dynamics. To better understand how community diversity is affected by complex interactions between its members, we developed a framework (Microbial community dIversity and Network Analysis, mina), a comprehensive framework for microbial community diversity analysis and network comparison. By defining and integrating network-derived community features, we greatly reduce noise-to-signal ratio for diversity analyses. A bootstrap and permutation-based method was implemented to assess community network dissimilarities and extract discriminative features in a statistically principled way.

r-msbackendmetabolights 1.4.2
Propagated dependencies: r-spectra@1.18.2 r-s4vectors@0.46.0 r-protgenerics@1.40.0 r-progress@1.2.3 r-curl@6.2.3 r-biocfilecache@2.16.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/RforMassSpectrometry/MsBackendMetaboLights
Licenses: Artistic License 2.0
Synopsis: Retrieve Mass Spectrometry Data from MetaboLights
Description:

MetaboLights is one of the main public repositories for storage of metabolomics experiments, which includes analysis results as well as raw data. The MsBackendMetaboLights package provides functionality to retrieve and represent mass spectrometry (MS) data from MetaboLights. Data files are downloaded and cached locally avoiding repetitive downloads. MS data from metabolomics experiments can thus be directly and seamlessly integrated into R-based analysis workflows with the Spectra and MsBackendMetaboLights package.

r-methylscaper 1.18.0
Propagated dependencies: r-summarizedexperiment@1.38.1 r-shinyjs@2.1.0 r-shinyfiles@0.9.3 r-shiny@1.10.0 r-seriation@1.5.7 r-seqinr@4.2-36 r-rfast@2.1.5.1 r-pwalign@1.4.0 r-data-table@1.17.4 r-biostrings@2.76.0 r-biocparallel@1.42.0
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-methylcc 1.24.1
Propagated dependencies: r-s4vectors@0.46.0 r-quadprog@1.5-8 r-minfi@1.54.1 r-magrittr@2.0.3 r-iranges@2.42.0 r-illuminahumanmethylation450kmanifest@0.4.0 r-illuminahumanmethylation450kanno-ilmn12-hg19@0.6.1 r-genomicranges@1.60.0 r-genefilter@1.90.0 r-flowsorted-blood-450k@1.46.0 r-dplyr@1.1.4 r-bumphunter@1.50.0 r-bsseq@1.44.1 r-biobase@2.68.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/stephaniehicks/methylCC/
Licenses: GPL 3
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-mammaprintdata 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://luigimarchionni.org/breastTSP.html
Licenses: Artistic License 2.0
Synopsis: RGLists from the Glas and Buyse breast cancer studies
Description:

Gene expression data for the two breast cancer cohorts published by Glas and Buyse in 2006. This cohorts were used to implement and validate the mammaPrint breast cancer test.

r-msstatsptm 2.12.0
Propagated dependencies: r-stringr@1.5.1 r-stringi@1.8.7 r-rcpp@1.0.14 r-plotly@4.10.4 r-msstatstmt@2.18.0 r-msstatsconvert@1.20.0 r-msstats@4.18.0 r-htmltools@0.5.8.1 r-gridextra@2.3 r-ggrepel@0.9.6 r-ggplot2@3.5.2 r-dplyr@1.1.4 r-data-table@1.17.4 r-checkmate@2.3.2 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MSstatsPTM
Licenses: Artistic License 2.0
Synopsis: Statistical Characterization of Post-translational Modifications
Description:

MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, SRM, and tandem mass tag (TMT) labeling. Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.

r-mugaexampledata 1.30.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MUGAExampleData
Licenses: GPL 3
Synopsis: Example {M}ouse {U}niversal {G}enotyping {A}rray data for genome reconstruction and quantitative trait locus mapping
Description:

This package contains example data for the MUGA array that is used by the R package DOQTL.

r-mu11ksuba-db 3.13.0
Propagated dependencies: r-org-mm-eg-db@3.21.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mu11ksuba.db
Licenses: Artistic License 2.0
Synopsis: Affymetrix Affymetrix Mu11KsubA Array annotation data (chip mu11ksuba)
Description:

Affymetrix Affymetrix Mu11KsubA Array annotation data (chip mu11ksuba) assembled using data from public repositories.

r-maqcexpression4plex 1.54.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/maqcExpression4plex
Licenses: GPL 2+ GPL 3+
Synopsis: Sample Expression Data - MAQC / HG18 - NimbleGen
Description:

Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene.

r-mu11ksubbprobe 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/mu11ksubbprobe
Licenses: LGPL 2.0+
Synopsis: Probe sequence data for microarrays of type mu11ksubb
Description:

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mu11KsubB\_probe\_tab.

r-maizecdf 2.18.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/maizecdf
Licenses: LGPL 2.0+
Synopsis: maizecdf
Description:

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

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Total results: 45109