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    / / /\ \ \ / / /  \ \_\\ \ \_/      \ \ \ \/___/
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/_/ /      / / /____\/ /       \ \_\\ \/___/ /
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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-makl 1.0.1
Propagated dependencies: r-grplasso@0.4-7 r-auc@0.3.2
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=MAKL
Licenses: GPL 3+
Build system: r
Synopsis: Multiple Approximate Kernel Learning (MAKL)
Description:

R package associated with the Multiple Approximate Kernel Learning (MAKL) algorithm proposed in <doi:10.1093/bioinformatics/btac241>. The algorithm fits multiple approximate kernel learning (MAKL) models that are fast, scalable and interpretable.

r-mulea 1.1.1
Propagated dependencies: r-tidyverse@2.0.0 r-tidygraph@1.3.1 r-tibble@3.3.0 r-stringi@1.8.7 r-scales@1.4.0 r-rlang@1.1.6 r-readr@2.1.6 r-rcpp@1.1.0 r-plyr@1.8.9 r-magrittr@2.0.4 r-ggraph@2.2.2 r-ggplot2@4.0.1 r-fgsea@1.36.0 r-dplyr@1.1.4 r-data-table@1.17.8
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://github.com/ELTEbioinformatics/mulea
Licenses: GPL 2
Build system: r
Synopsis: Enrichment Analysis Using Multiple Ontologies and False Discovery Rate
Description:

Background - Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. Results - mulea employs a progressive empirical false discovery rate (eFDR) method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. mulea expands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis, mulea provides gene sets (in standardised GMT format) for 27 model organisms, covering 22 ontology types from 16 databases and various identifiers resulting in almost 900 files. Additionally, the muleaData ExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally, mulea's architecture allows for easy integration of user-defined ontologies, or GMT files from external sources (e.g., MSigDB or Enrichr), expanding its applicability across diverse research areas. Conclusions - mulea is distributed as a CRAN R package. It offers researchers a powerful and flexible toolkit for functional enrichment analysis, addressing limitations of traditional tools with its progressive eFDR and by supporting a variety of ontologies. Overall, mulea fosters the exploration of diverse biological questions across various model organisms.

r-mergingtools 1.0.1
Propagated dependencies: r-tidyr@1.3.1 r-stringr@1.6.0 r-rlang@1.1.6 r-purrr@1.2.0 r-mass@7.3-65 r-dplyr@1.1.4
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=mergingTools
Licenses: GPL 3
Build system: r
Synopsis: Tools to Merge Hardware Event Monitors (HEMs) Coming from Separate Subexperiments into One Single Dataframe
Description:

Implementation of two tools to merge Hardware Event Monitors (HEMs) from different subexperiments. Hardware Reading and Merging (HRM), which uses order statistics to merge; and MUlti-Correlation HEM (MUCH) which merges using a multivariate normal distribution. The reference paper for HRM is: S. Vilardell, I. Serra, R. Santalla, E. Mezzetti, J. Abella and F. J. Cazorla, "HRM: Merging Hardware Event Monitors for Improved Timing Analysis of Complex MPSoCs," in IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, vol. 39, no. 11, pp. 3662-3673, Nov. 2020, <doi:10.1109/TCAD.2020.3013051>. For MUCH: S. Vilardell, I. Serra, E. Mezzetti, J. Abella, and F. J. Cazorla. 2021. "MUCH: exploiting pairwise hardware event monitor correlations for improved timing analysis of complex MPSoCs". In Proceedings of the 36th Annual ACM Symposium on Applied Computing (SAC 21). Association for Computing Machinery. <doi:10.1145/3412841.3441931>. This work has been supported by the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 772773).

r-micropan 2.1
Propagated dependencies: r-tibble@3.3.0 r-stringr@1.6.0 r-rlang@1.1.6 r-microseq@2.1.7 r-igraph@2.2.1 r-dplyr@1.1.4
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=micropan
Licenses: GPL 2
Build system: r
Synopsis: Microbial Pan-Genome Analysis
Description:

This package provides a collection of functions for computations and visualizations of microbial pan-genomes.

r-margins 0.3.28
Propagated dependencies: r-prediction@0.3.18 r-mass@7.3-65 r-data-table@1.17.8
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://github.com/bbolker/margins
Licenses: Expat
Build system: r
Synopsis: Marginal Effects for Model Objects
Description:

An R port of the margins command from Stata', which can be used to calculate marginal (or partial) effects from model objects.

r-mortalitylaws 2.1.3
Propagated dependencies: r-tidyr@1.3.1 r-rvest@1.0.5 r-rcurl@1.98-1.17 r-pbapply@1.7-4 r-minpack-lm@1.2-4 r-httr@1.4.7
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://github.com/mpascariu/MortalityLaws
Licenses: Expat
Build system: r
Synopsis: Parametric Mortality Models, Life Tables and HMD
Description:

Fit the most popular human mortality laws', and construct full and abridge life tables given various input indices. A mortality law is a parametric function that describes the dying-out process of individuals in a population during a significant portion of their life spans. For a comprehensive review of the most important mortality laws see Tabeau (2001) <doi:10.1007/0-306-47562-6_1>. Practical functions for downloading data from various human mortality databases are provided as well.

r-mdmapr 0.2.3
Propagated dependencies: r-xfun@0.54 r-writexl@1.5.4 r-shinywidgets@0.9.0 r-shinyjs@2.1.0 r-shinydashboard@0.7.3 r-shiny@1.11.1 r-rmysql@0.11.1 r-readxl@1.4.5 r-reactable@0.4.5 r-plotly@4.11.0 r-leaflet-extras@2.0.1 r-leaflet@2.2.3 r-htmlwidgets@1.6.4 r-htmltools@0.5.8.1 r-ggplot2@4.0.1 r-dt@0.34.0 r-dplyr@1.1.4 r-dbi@1.2.3 r-bslib@0.9.0 r-berryfunctions@1.22.13
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://github.com/HannerLab/MDMAPR
Licenses: GPL 3
Build system: r
Synopsis: Molecular Detection Mapping and Analysis Platform
Description:

Runs a Shiny web application that merges raw qPCR fluorescence data with related metadata to visualize species presence/absence detection patterns and assess data quality. The application calculates threshold values from raw fluorescence data using a method based on the second derivative method, Luu-The et al (2005) <doi:10.2144/05382RR05>, and utilizes the âchipPCRâ package by Rödiger, Burdukiewicz, & Schierack (2015) <doi:10.1093/bioinformatics/btv205> to calculate Cq values. The application has the ability to connect to a custom developed MySQL database to populate the applications interface. The application allows users to interact with visualizations such as a dynamic map, amplification curves and standard curves, that allow for zooming and/or filtering. It also enables the generation of customized exportable reports based on filtered mapping data.

r-mintplates 1.0.1
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: http://www.bio-inf.cn/
Licenses: GPL 2+
Build system: r
Synopsis: Encode "License-Plates" from Sequences and Decode Them Back
Description:

It can be used to create/encode molecular "license-plates" from sequences and to also decode the "license-plates" back to sequences. While initially created for transfer RNA-derived small fragments (tRFs), this tool can be used for any genomic sequences including but not limited to: tRFs, microRNAs, etc. The detailed information can reference to Pliatsika V, Loher P, Telonis AG, Rigoutsos I (2016) <doi:10.1093/bioinformatics/btw194>. It can also be used to annotate tRFs. The detailed information can reference to Loher P, Telonis AG, Rigoutsos I (2017) <doi:10.1038/srep41184>.

r-meanshiftr 0.56
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: http://meanmean.me/meanshift/r/cran/2016/08/28/meanShiftR.html
Licenses: GPL 2+
Build system: r
Synopsis: Computationally Efficient Mean Shift Implementation
Description:

This package performs mean shift classification using linear and k-d tree based nearest neighbor implementations for the Gaussian, Epanechnikov, and biweight product kernels.

r-mmr 0.1.0
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://github.com/stevecondylios/mmr
Licenses: Expat
Build system: r
Synopsis: Matrix Multiplication on Data.frames
Description:

Simple helpers for matrix multiplication on data.frames. These allow for more concise code during low level mathematical operations, and help ensure code is more easily read, understood, and serviced.

r-multiassetoptions 0.1-2
Propagated dependencies: r-matrix@1.7-4
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=multiAssetOptions
Licenses: GPL 2 GPL 3
Build system: r
Synopsis: Finite Difference Method for Multi-Asset Option Valuation
Description:

Efficient finite difference method for valuing European and American multi-asset options.

r-modmarg 0.9.6
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://github.com/anniejw6/modmarg
Licenses: GPL 3
Build system: r
Synopsis: Calculating Marginal Effects and Levels with Errors
Description:

Calculate predicted levels and marginal effects, using the delta method to calculate standard errors. This is an R-based version of the margins command from Stata.

r-marble 0.0.3
Propagated dependencies: r-rcpparmadillo@15.2.2-1 r-rcpp@1.1.0
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://github.com/xilustat/marble
Licenses: GPL 2
Build system: r
Synopsis: Robust Marginal Bayesian Variable Selection for Gene-Environment Interactions
Description:

Recently, multiple marginal variable selection methods have been developed and shown to be effective in Gene-Environment interactions studies. We propose a novel marginal Bayesian variable selection method for Gene-Environment interactions studies. In particular, our marginal Bayesian method is robust to data contamination and outliers in the outcome variables. With the incorporation of spike-and-slab priors, we have implemented the Gibbs sampler based on Markov Chain Monte Carlo. The core algorithms of the package have been developed in C++'.

r-mri 1.0.1
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=mri
Licenses: GPL 2+
Build system: r
Synopsis: Modified Rand and Wallace Indices
Description:

It provides functions to compute the values of different modifications of the Rand and Wallace indices. The indices are used to measure the stability or similarity of two partitions obtained on two different sets of units with a non-empty intercept. Splitting and merging of clusters can (depends on the selected index) have a different effect on the value of the indices. The indices are proposed in Cugmas and Ferligoj (2018) <http://ibmi.mf.uni-lj.si/mz/2018/no-1/Cugmas2018.pdf>.

r-mldatar 1.0.1
Propagated dependencies: r-workflows@1.3.0 r-varhandle@2.0.6 r-rsample@1.3.1 r-recipes@1.3.1 r-ranger@0.17.0 r-parsnip@1.3.3 r-oddsplotty@1.0.2 r-ggplot2@4.0.1 r-dplyr@1.1.4 r-confusiontabler@1.0.4 r-caret@7.0-1
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=MLDataR
Licenses: Expat
Build system: r
Synopsis: Collection of Machine Learning Datasets for Supervised Machine Learning
Description:

This package contains a collection of datasets for working with machine learning tasks. It will contain datasets for supervised machine learning Jiang (2020)<doi:10.1016/j.beth.2020.05.002> and will include datasets for classification and regression. The aim of this package is to use data generated around health and other domains.

r-mhtrajectoryr 1.0.1
Propagated dependencies: r-mgcv@1.9-4
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=MHTrajectoryR
Licenses: GPL 2+
Build system: r
Synopsis: Bayesian Model Selection in Logistic Regression for the Detection of Adverse Drug Reactions
Description:

Spontaneous adverse event reports have a high potential for detecting adverse drug reactions. However, due to their dimension, the analysis of such databases requires statistical methods. We propose to use a logistic regression whose sparsity is viewed as a model selection challenge. Since the model space is huge, a Metropolis-Hastings algorithm carries out the model selection by maximizing the BIC criterion.

r-metaprotr 1.2.2
Propagated dependencies: r-tidyverse@2.0.0 r-stringr@1.6.0 r-reshape2@1.4.5 r-ggrepel@0.9.6 r-ggforce@0.5.0 r-dplyr@1.1.4 r-dendextend@1.19.1 r-ade4@1.7-23
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://forgemia.inra.fr/pappso/metaprotr
Licenses: GPL 3
Build system: r
Synopsis: Metaproteomics Post-Processing Analysis
Description:

Set of tools for descriptive analysis of metaproteomics data generated from high-throughput mass spectrometry instruments. These tools allow to cluster peptides and proteins abundance, expressed as spectral counts, and to manipulate them in groups of metaproteins. This information can be represented using multiple visualization functions to portray the global metaproteome landscape and to differentiate samples or conditions, in terms of abundance of metaproteins, taxonomic levels and/or functional annotation. The provided tools allow to implement flexible analytical pipelines that can be easily applied to studies interested in metaproteomics analysis.

r-mmdai 2.0.0
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=MMDai
Licenses: GPL 2+
Build system: r
Synopsis: Multivariate Multinomial Distribution Approximation and Imputation for Incomplete Categorical Data
Description:

This package provides a method to impute the missingness in categorical data. Details see the paper <doi:10.4310/SII.2020.v13.n1.a2>.

r-multiselect 0.1.0
Propagated dependencies: r-hmisc@5.2-4
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=multiselect
Licenses: GPL 2
Build system: r
Synopsis: Selecting Combinations of Predictors by Leveraging Multiple AUCs for an Ordered Multilevel Outcome
Description:

Uses multiple AUCs to select a combination of predictors when the outcome has multiple (ordered) levels and the focus is discriminating one particular level from the others. This method is most naturally applied to settings where the outcome has three levels. (Meisner, A, Parikh, CR, and Kerr, KF (2017) <http://biostats.bepress.com/uwbiostat/paper423/>.).

r-mcprogress 0.1.1
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://github.com/myles-lewis/mcprogress
Licenses: GPL 3+
Build system: r
Synopsis: Progress Bars and Messages for Parallel Processes
Description:

This package provides tools for monitoring progress during parallel processing. Lightweight package which acts as a wrapper around mclapply() and adds a progress bar to it in RStudio or Linux environments. Simply replace your original call to mclapply() with pmclapply(). A progress bar can also be displayed during parallelisation via the foreach package. Also included are functions to safely print messages (including error messages) from within parallelised code, which can be useful for debugging parallelised R code.

r-meme 0.2.4
Propagated dependencies: r-sysfonts@0.8.9 r-showtext@0.9-7 r-magick@2.9.0 r-gridgraphics@0.5-1 r-ggplot2@4.0.1
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://github.com/GuangchuangYu/meme/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Create Meme
Description:

The word Meme was originated from the book, The Selfish Gene', authored by Richard Dawkins (1976). It is a unit of culture that is passed from one generation to another and correlates to the gene, the unit of physical heredity. The internet memes are captioned photos that are intended to be funny, ridiculous. Memes behave like infectious viruses and travel from person to person quickly through social media. The meme package allows users to make custom memes.

r-maxstablepca 0.1.2
Propagated dependencies: r-nloptr@2.2.1
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=maxstablePCA
Licenses: Expat
Build system: r
Synopsis: Apply a PCA Like Procedure Suited for Multivariate Extreme Value Distributions
Description:

Dimension reduction for multivariate data of extreme events with a PCA like procedure as described in Reinbott, Janà en, (2024), <doi:10.48550/arXiv.2408.10650>. Tools for necessary transformations of the data are provided.

r-mero 0.1.2
Propagated dependencies: r-progress@1.2.3 r-missforest@1.6.1 r-ggpubr@0.6.2 r-foreach@1.5.2 r-doparallel@1.0.17
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=MERO
Licenses: GPL 3
Build system: r
Synopsis: Performing Monte Carlo Expectation Maximization Random Forest Imputation for Biological Data
Description:

Perform missing value imputation for biological data using the random forest algorithm, the imputation aim to keep the original mean and standard deviation consistent after imputation.

r-msprt 3.0
Propagated dependencies: r-nleqslv@3.3.5 r-iterators@1.0.14 r-ggpubr@0.6.2 r-ggplot2@4.0.1 r-foreach@1.5.2 r-doparallel@1.0.17
Channel: guix-cran
Location: guix-cran/packages/m.scm (guix-cran packages m)
Home page: https://cran.r-project.org/package=MSPRT
Licenses: GPL 2+
Build system: r
Synopsis: Modified Sequential Probability Ratio Test (MSPRT)
Description:

Given the maximum available sample size (N) for an experiment, and the target levels of Type I and II error probabilities, this package designs a modified SPRT (MSPRT). For any designed MSPRT the package can also obtain its operating characteristics and implement the test for a given sequentially observed data. The MSPRT is defined in a manner very similar to Wald's initial proposal. The proposed test has shown evidence of reducing the average sample size required to perform statistical hypothesis tests at specified levels of significance and power. Currently, the package implements one-sample proportion tests, one and two-sample z tests, and one and two-sample t tests. A brief user guidance for this package is provided below. One can also refer to the supplemental information for the same.

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