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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-meskit 1.20.0
Propagated dependencies: r-tidyr@1.3.1 r-s4vectors@0.46.0 r-rcolorbrewer@1.1-3 r-pracma@2.4.4 r-phangorn@2.12.1 r-mclust@6.1.1 r-iranges@2.42.0 r-ggridges@0.5.6 r-ggrepel@0.9.6 r-ggplot2@3.5.2 r-dplyr@1.1.4 r-data-table@1.17.4 r-cowplot@1.1.3 r-complexheatmap@2.24.0 r-circlize@0.4.16 r-biostrings@2.76.0 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://bioconductor.org/packages/MesKit
Licenses: GPL 3
Synopsis: tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic alterations
Description:

MesKit provides commonly used analysis and visualization modules based on mutational data generated by multi-region sequencing (MRS). This package allows to depict mutational profiles, measure heterogeneity within or between tumors from the same patient, track evolutionary dynamics, as well as characterize mutational patterns on different levels. Shiny application was also developed for a need of GUI-based analysis. As a handy tool, MesKit can facilitate the interpretation of tumor heterogeneity and the understanding of evolutionary relationship between regions in MRS study.

r-m6aboost 1.16.0
Propagated dependencies: r-s4vectors@0.46.0 r-rtracklayer@1.68.0 r-iranges@2.42.0 r-genomicranges@1.60.0 r-experimenthub@2.16.0 r-dplyr@1.1.4 r-bsgenome@1.76.0 r-biostrings@2.76.0 r-adabag@5.0
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
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-methreg 1.20.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MethReg
Licenses: GPL 3
Synopsis: Assessing the regulatory potential of DNA methylation regions or sites on gene transcription
Description:

Epigenome-wide association studies (EWAS) detects a large number of DNA methylation differences, often hundreds of differentially methylated regions and thousands of CpGs, that are significantly associated with a disease, many are located in non-coding regions. Therefore, there is a critical need to better understand the functional impact of these CpG methylations and to further prioritize the significant changes. MethReg is an R package for integrative modeling of DNA methylation, target gene expression and transcription factor binding sites data, to systematically identify and rank functional CpG methylations. MethReg evaluates, prioritizes and annotates CpG sites with high regulatory potential using matched methylation and gene expression data, along with external TF-target interaction databases based on manually curation, ChIP-seq experiments or gene regulatory network analysis.

r-microbiomebenchmarkdata 1.12.0
Propagated dependencies: r-treesummarizedexperiment@2.16.1 r-summarizedexperiment@1.38.1 r-s4vectors@0.46.0 r-biocfilecache@2.16.0 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/waldronlab/MicrobiomeBenchmarkData
Licenses: Artistic License 2.0
Synopsis: Datasets for benchmarking in microbiome research
Description:

The MicrobiomeBenchmarkData package provides functionality to access microbiome datasets suitable for benchmarking. These datasets have some biological truth, which allows to have expected results for comparison. The datasets come from various published sources and are provided as TreeSummarizedExperiment objects. Currently, only datasets suitable for benchmarking differential abundance methods are available.

r-msquality 1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://www.github.com/tnaake/MsQuality/
Licenses: GPL 3
Synopsis: MsQuality - Quality metric calculation from Spectra and MsExperiment objects
Description:

The MsQuality provides functionality to calculate quality metrics for mass spectrometry-derived, spectral data at the per-sample level. MsQuality relies on the mzQC framework of quality metrics defined by the Human Proteom Organization-Proteomics Standards Initiative (HUPO-PSI). These metrics quantify the quality of spectral raw files using a controlled vocabulary. The package is especially addressed towards users that acquire mass spectrometry data on a large scale (e.g. data sets from clinical settings consisting of several thousands of samples). The MsQuality package allows to calculate low-level quality metrics that require minimum information on mass spectrometry data: retention time, m/z values, and associated intensities. MsQuality relies on the Spectra package, or alternatively the MsExperiment package, and its infrastructure to store spectral data.

r-mbqn 2.22.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/arianeschad/mbqn
Licenses: FSDG-compatible
Synopsis: Mean/Median-balanced quantile normalization
Description:

Modified quantile normalization for omics or other matrix-like data distorted in location and scale.

r-mafdb-exac-r1-0-nontcga-grch38 3.10.0
Propagated dependencies: r-s4vectors@0.46.0 r-iranges@2.42.0 r-genomicscores@2.20.0 r-genomicranges@1.60.0 r-genomeinfodb@1.44.0 r-bsgenome@1.76.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MafDb.ExAC.r1.0.nonTCGA.GRCh38
Licenses: Artistic License 2.0
Synopsis: Minor allele frequency data from ExAC release 1.0 subset of nonTCGA exomes for GRCh38
Description:

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

r-mgu74av2cdf 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/mgu74av2cdf
Licenses: LGPL 2.0+
Synopsis: mgu74av2cdf
Description:

This package provides a package containing an environment representing the MG_U74Av2.CDF file.

r-mpfe 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MPFE
Licenses: GPL 3+
Synopsis: Estimation of the amplicon methylation pattern distribution from bisulphite sequencing data
Description:

Estimate distribution of methylation patterns from a table of counts from a bisulphite sequencing experiment given a non-conversion rate and read error rate.

r-mumosa 1.18.0
Propagated dependencies: r-uwot@0.2.3 r-summarizedexperiment@1.38.1 r-singlecellexperiment@1.30.1 r-scuttle@1.18.0 r-scran@1.36.0 r-scaledmatrix@1.16.0 r-s4vectors@0.46.0 r-metapod@1.16.0 r-matrix@1.7-3 r-iranges@2.42.0 r-igraph@2.1.4 r-delayedmatrixstats@1.30.0 r-delayedarray@0.34.1 r-biocsingular@1.24.0 r-biocparallel@1.42.0 r-biocneighbors@2.2.0 r-biocgenerics@0.54.0 r-beachmat@2.24.0 r-batchelor@1.24.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://bioconductor.org/packages/mumosa
Licenses: GPL 3
Synopsis: Multi-Modal Single-Cell Analysis Methods
Description:

Assorted utilities for multi-modal analyses of single-cell datasets. Includes functions to combine multiple modalities for downstream analysis, perform MNN-based batch correction across multiple modalities, and to compute correlations between assay values for different modalities.

r-mgu74cv2probe 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/mgu74cv2probe
Licenses: LGPL 2.0+
Synopsis: Probe sequence data for microarrays of type mgu74cv2
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 MG-U74Cv2\_probe\_tab.

r-mm24kresogen-db 2.5.0
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/mm24kresogen.db
Licenses: Artistic License 2.0
Synopsis: RNG_MRC Mouse Pangenomic 24k Set annotation data (chip mm24kresogen)
Description:

RNG_MRC Mouse Pangenomic 24k Set annotation data (chip mm24kresogen) assembled using data from public repositories.

r-mouse430a2probe 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/mouse430a2probe
Licenses: LGPL 2.0+
Synopsis: Probe sequence data for microarrays of type mouse430a2
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 Mouse430A\_2\_probe\_tab.

r-mirsm 2.6.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/zhangjunpeng411/miRSM
Licenses: GPL 3
Synopsis: Inferring miRNA sponge modules in heterogeneous data
Description:

The package aims to identify miRNA sponge or ceRNA modules in heterogeneous data. It provides several functions to study miRNA sponge modules at single-sample and multi-sample levels, including popular methods for inferring gene modules (candidate miRNA sponge or ceRNA modules), and two functions to identify miRNA sponge modules at single-sample and multi-sample levels, as well as several functions to conduct modular analysis of miRNA sponge modules.

r-mu11ksubacdf 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/mu11ksubacdf
Licenses: LGPL 2.0+
Synopsis: mu11ksubacdf
Description:

This package provides a package containing an environment representing the Mu11KsubA.CDF file.

r-mirlab 1.40.0
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-micsqtl 1.8.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MICSQTL
Licenses: GPL 3
Synopsis: MICSQTL (Multi-omic deconvolution, Integration and Cell-type-specific Quantitative Trait Loci)
Description:

Our pipeline, MICSQTL, utilizes scRNA-seq reference and bulk transcriptomes to estimate cellular composition in the matched bulk proteomes. The expression of genes and proteins at either bulk level or cell type level can be integrated by Angle-based Joint and Individual Variation Explained (AJIVE) framework. Meanwhile, MICSQTL can perform cell-type-specic quantitative trait loci (QTL) mapping to proteins or transcripts based on the input of bulk expression data and the estimated cellular composition per molecule type, without the need for single cell sequencing. We use matched transcriptome-proteome from human brain frontal cortex tissue samples to demonstrate the input and output of our tool.

r-mogene20sttranscriptcluster-db 8.8.0
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/mogene20sttranscriptcluster.db
Licenses: Artistic License 2.0
Synopsis: Affymetrix mogene20 annotation data (chip mogene20sttranscriptcluster)
Description:

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

r-merfishdata 1.12.0
Propagated dependencies: r-summarizedexperiment@1.38.1 r-spatialexperiment@1.18.1 r-singlecellexperiment@1.30.1 r-s4vectors@0.46.0 r-hdf5array@1.36.0 r-experimenthub@2.16.0 r-ebimage@4.50.0 r-bumpymatrix@1.16.0 r-annotationhub@3.16.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://github.com/ccb-hms/MerfishData
Licenses: Artistic License 2.0
Synopsis: Collection of public MERFISH datasets
Description:

MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis.

r-messina 1.46.0
Propagated dependencies: r-survival@3.8-3 r-rcpp@1.0.14 r-plyr@1.8.9 r-ggplot2@3.5.2 r-foreach@1.5.2
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/messina
Licenses: FSDG-compatible
Synopsis: Single-gene classifiers and outlier-resistant detection of differential expression for two-group and survival problems
Description:

Messina is a collection of algorithms for constructing optimally robust single-gene classifiers, and for identifying differential expression in the presence of outliers or unknown sample subgroups. The methods have application in identifying lead features to develop into clinical tests (both diagnostic and prognostic), and in identifying differential expression when a fraction of samples show unusual patterns of expression.

r-macorrplot 1.80.0
Propagated dependencies: r-lattice@0.22-7
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=15799785
Licenses: GPL 2+
Synopsis: Visualize artificial correlation in microarray data
Description:

Graphically displays correlation in microarray data that is due to insufficient normalization.

r-metnet 1.28.0
Channel: guix-bioc
Location: guix-bioc/packages/m.scm (guix-bioc packages m)
Home page: https://bioconductor.org/packages/MetNet
Licenses: GPL 3+
Synopsis: Inferring metabolic networks from untargeted high-resolution mass spectrometry data
Description:

MetNet contains functionality to infer metabolic network topologies from quantitative data and high-resolution mass/charge information. Using statistical models (including correlation, mutual information, regression and Bayes statistics) and quantitative data (intensity values of features) adjacency matrices are inferred that can be combined to a consensus matrix. Mass differences calculated between mass/charge values of features will be matched against a data frame of supplied mass/charge differences referring to transformations of enzymatic activities. In a third step, the two levels of information are combined to form a adjacency matrix inferred from both quantitative and structure information.

r-mirnatarget 1.48.0
Propagated dependencies: r-biobase@2.68.0
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-mirna20cdf 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/mirna20cdf
Licenses: LGPL 2.0+
Synopsis: mirna20cdf
Description:

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

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Total results: 45109