_            _    _        _         _
      /\ \         /\ \ /\ \     /\_\      / /\
      \_\ \       /  \ \\ \ \   / / /     / /  \
      /\__ \     / /\ \ \\ \ \_/ / /     / / /\ \__
     / /_ \ \   / / /\ \ \\ \___/ /     / / /\ \___\
    / / /\ \ \ / / /  \ \_\\ \ \_/      \ \ \ \/___/
   / / /  \/_// / /   / / / \ \ \        \ \ \
  / / /      / / /   / / /   \ \ \   _    \ \ \
 / / /      / / /___/ / /     \ \ \ /_/\__/ / /
/_/ /      / / /____\/ /       \ \_\\ \/___/ /
\_\/       \/_________/         \/_/ \_____\/

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 search send a patch to ~whereiseveryone/toys@lists.sr.ht adding your channel as an entry in channels.scm.


r-celegans-db 3.13.0
Propagated dependencies: r-org-ce-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/celegans.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix Celegans Array annotation data (chip celegans)
Description:

Affymetrix Affymetrix Celegans Array annotation data (chip celegans) assembled using data from public repositories.

r-cellmixs 1.28.0
Propagated dependencies: r-viridis@0.6.5 r-tidyr@1.3.2 r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-scater@1.38.0 r-purrr@1.2.1 r-magrittr@2.0.4 r-ksamples@1.2-12 r-ggridges@0.5.7 r-ggplot2@4.0.2 r-dplyr@1.2.0 r-cowplot@1.2.0 r-biocparallel@1.44.0 r-biocneighbors@2.4.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/almutlue/CellMixS
Licenses: FSDG-compatible
Build system: r
Synopsis: Evaluate Cellspecific Mixing
Description:

CellMixS provides metrics and functions to evaluate batch effects, data integration and batch effect correction in single cell trancriptome data with single cell resolution. Results can be visualized and summarised on different levels, e.g. on cell, celltype or dataset level.

r-chemminedrugs 1.0.2
Propagated dependencies: r-rsqlite@2.4.6 r-chemminer@3.62.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/ChemmineDrugs
Licenses: Artistic License 2.0
Build system: r
Synopsis: DrugBank data set
Description:

An annotation package for use with ChemmineR. This package includes data from DrugBank. DUD data can be downloaded using the "DUD()" function in ChemmineR.

r-ccdata 1.38.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/ccdata
Licenses: Expat
Build system: r
Synopsis: Data for Combination Connectivity Mapping (ccmap) Package
Description:

This package contains microarray gene expression data generated from the Connectivity Map build 02 and LINCS l1000. The data are used by the ccmap package to find drugs and drug combinations to mimic or reverse a gene expression signature.

r-ctdata 1.12.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CTdata
Licenses: Artistic License 2.0
Build system: r
Synopsis: Data companion to CTexploreR
Description:

Data from publicly available databases (GTEx, CCLE, TCGA and ENCODE) that go with CTexploreR in order to re-define a comprehensive and thoroughly curated list of CT genes and their main characteristics.

r-clst 1.60.0
Propagated dependencies: r-roc@1.86.0 r-lattice@0.22-9
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/clst
Licenses: GPL 3
Build system: r
Synopsis: Classification by local similarity threshold
Description:

Package for modified nearest-neighbor classification based on calculation of a similarity threshold distinguishing within-group from between-group comparisons.

r-conumee 1.46.0
Propagated dependencies: r-seqinfo@1.0.0 r-rtracklayer@1.70.1 r-minfi@1.56.0 r-iranges@2.44.0 r-illuminahumanmethylationepicmanifest@0.3.0 r-illuminahumanmethylationepicanno-ilm10b2-hg19@0.6.0 r-illuminahumanmethylation450kmanifest@0.4.0 r-illuminahumanmethylation450kanno-ilmn12-hg19@0.6.1 r-genomicranges@1.62.1 r-dnacopy@1.84.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/conumee
Licenses: GPL 2+
Build system: r
Synopsis: Enhanced copy-number variation analysis using Illumina DNA methylation arrays
Description:

This package contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using Illumina 450k or EPIC methylation arrays.

r-celegansprobe 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/celegansprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type celegans
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 C\_elegans\_probe\_tab.

r-colonca 1.54.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/colonCA
Licenses: LGPL 2.0+
Build system: r
Synopsis: exprSet for Alon et al. (1999) colon cancer data
Description:

exprSet for Alon et al. (1999) colon cancer data.

r-crisprshiny 1.8.0
Propagated dependencies: r-waiter@0.2.5-1.927501b r-shinyjs@2.1.1 r-shinybs@0.63.0 r-shiny@1.11.1 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-pwalign@1.6.0 r-htmlwidgets@1.6.4 r-dt@0.34.0 r-crisprviz@1.14.0 r-crisprscore@1.16.0 r-crisprdesign@1.14.0 r-crisprbase@1.16.0 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/crisprVerse/crisprShiny
Licenses: Expat
Build system: r
Synopsis: Exploring curated CRISPR gRNAs via Shiny
Description:

This package provides means to interactively visualize guide RNAs (gRNAs) in GuideSet objects via Shiny application. This GUI can be self-contained or as a module within a larger Shiny app. The content of the app reflects the annotations present in the passed GuideSet object, and includes intuitive tools to examine, filter, and export gRNAs, thereby making gRNA design more user-friendly.

r-clippda 1.62.0
Propagated dependencies: r-statmod@1.5.1 r-scatterplot3d@0.3-45 r-rgl@1.3.34 r-limma@3.66.0 r-lattice@0.22-9 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: http://www.cancerstudies.bham.ac.uk/crctu/CLIPPDA.shtml
Licenses: FSDG-compatible
Build system: r
Synopsis: package for the clinical proteomic profiling data analysis
Description:

This package provides methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations.

r-discordant 1.36.0
Propagated dependencies: r-rcpp@1.1.1 r-mass@7.3-65 r-gtools@3.9.5 r-dplyr@1.2.0 r-biwt@1.0.1 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://github.com/siskac/discordant
Licenses: GPL 3
Build system: r
Synopsis: The Discordant Method: A Novel Approach for Differential Correlation
Description:

Discordant is an R package that identifies pairs of features that correlate differently between phenotypic groups, with application to -omics data sets. Discordant uses a mixture model that “bins” molecular feature pairs based on their type of coexpression or coabbundance. Algorithm is explained further in "Differential Correlation for Sequencing Data"" (Siska et al. 2016).

r-differentialregulation 2.10.0
Propagated dependencies: r-tximport@1.38.2 r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-rcpparmadillo@15.2.3-1 r-rcpp@1.1.1 r-matrix@1.7-4 r-mass@7.3-65 r-gridextra@2.3 r-ggplot2@4.0.2 r-foreach@1.5.2 r-dorng@1.8.6.3 r-doparallel@1.0.17 r-data-table@1.18.2.1 r-bandits@1.26.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://github.com/SimoneTiberi/DifferentialRegulation
Licenses: GPL 3
Build system: r
Synopsis: Differentially regulated genes from scRNA-seq data
Description:

DifferentialRegulation is a method for detecting differentially regulated genes between two groups of samples (e.g., healthy vs. disease, or treated vs. untreated samples), by targeting differences in the balance of spliced and unspliced mRNA abundances, obtained from single-cell RNA-sequencing (scRNA-seq) data. From a mathematical point of view, DifferentialRegulation accounts for the sample-to-sample variability, and embeds multiple samples in a Bayesian hierarchical model. Furthermore, our method also deals with two major sources of mapping uncertainty: i) ambiguous reads, compatible with both spliced and unspliced versions of a gene, and ii) reads mapping to multiple genes. In particular, ambiguous reads are treated separately from spliced and unsplced reads, while reads that are compatible with multiple genes are allocated to the gene of origin. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques (Metropolis-within-Gibbs).

r-davidtiling 1.52.0
Propagated dependencies: r-tilingarray@1.88.0 r-go-db@3.22.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: http://www.ebi.ac.uk/huber
Licenses: LGPL 2.0+
Build system: r
Synopsis: Data and analysis scripts for David, Huber et al. yeast tiling array paper
Description:

This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory.

r-dewseq 1.26.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-r-utils@2.13.0 r-genomicranges@1.62.1 r-deseq2@1.50.2 r-data-table@1.18.2.1 r-biocparallel@1.44.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://github.com/EMBL-Hentze-group/DEWSeq/
Licenses: LGPL 3+
Build system: r
Synopsis: Differential Expressed Windows Based on Negative Binomial Distribution
Description:

DEWSeq is a sliding window approach for the analysis of differentially enriched binding regions eCLIP or iCLIP next generation sequencing data.

r-damirseq 2.24.0
Propagated dependencies: r-sva@3.58.0 r-summarizedexperiment@1.40.0 r-seqinfo@1.0.0 r-rsnns@0.4-18 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-randomforest@4.7-1.2 r-plyr@1.8.9 r-plsvarsel@0.10.0 r-pls@2.9-0 r-pheatmap@1.0.13 r-mass@7.3-65 r-lubridate@1.9.5 r-limma@3.66.0 r-kknn@1.4.1 r-ineq@0.2-13 r-hmisc@5.2-5 r-ggplot2@4.0.2 r-fselector@0.34 r-factominer@2.13 r-edger@4.8.2 r-edaseq@2.44.0 r-e1071@1.7-17 r-deseq2@1.50.2 r-corrplot@0.95 r-caret@7.0-1 r-arm@1.14-4
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DaMiRseq
Licenses: GPL 2+
Build system: r
Synopsis: Data Mining for RNA-seq data: normalization, feature selection and classification
Description:

The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them for both binary and multi-class classification purposes. The package accepts any kind of data presented as a table of raw counts and allows including both continous and factorial variables that occur with the experimental setting. A series of functions enable the user to clean up the data by filtering genomic features and samples, to adjust data by identifying and removing the unwanted source of variation (i.e. batches and confounding factors) and to select the best predictors for modeling. Finally, a "stacking" ensemble learning technique is applied to build a robust classification model. Every step includes a checkpoint that the user may exploit to assess the effects of data management by looking at diagnostic plots, such as clustering and heatmaps, RLE boxplots, MDS or correlation plot.

r-dart 1.60.0
Propagated dependencies: r-igraph@2.2.2
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DART
Licenses: GPL 2
Build system: r
Synopsis: Denoising Algorithm based on Relevance network Topology
Description:

Denoising Algorithm based on Relevance network Topology (DART) is an algorithm designed to evaluate the consistency of prior information molecular signatures (e.g in-vitro perturbation expression signatures) in independent molecular data (e.g gene expression data sets). If consistent, a pruning network strategy is then used to infer the activation status of the molecular signature in individual samples.

r-dks 1.58.0
Propagated dependencies: r-cubature@2.1.4-1
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/dks
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: The double Kolmogorov-Smirnov package for evaluating multiple testing procedures
Description:

The dks package consists of a set of diagnostic functions for multiple testing methods. The functions can be used to determine if the p-values produced by a multiple testing procedure are correct. These functions are designed to be applied to simulated data. The functions require the entire set of p-values from multiple simulated studies, so that the joint distribution can be evaluated.

r-dnea 1.2.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-netgsa@4.0.7 r-matrix@1.7-4 r-janitor@2.2.1 r-igraph@2.2.2 r-glasso@1.11 r-gdata@3.0.1 r-dplyr@1.2.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://github.com/Karnovsky-Lab/DNEA
Licenses: Expat
Build system: r
Synopsis: Differential Network Enrichment Analysis for Biological Data
Description:

The DNEA R package is the latest implementation of the Differential Network Enrichment Analysis algorithm and is the successor to the Filigree Java-application described in Iyer et al. (2020). The package is designed to take as input an m x n expression matrix for some -omics modality (ie. metabolomics, lipidomics, proteomics, etc.) and jointly estimate the biological network associations of each condition using the DNEA algorithm described in Ma et al. (2019). This approach provides a framework for data-driven enrichment analysis across two experimental conditions that utilizes the underlying correlation structure of the data to determine feature-feature interactions.

r-doubletrouble 1.12.0
Propagated dependencies: r-syntenet@1.14.0 r-rlang@1.1.7 r-msa2dist@1.16.0 r-mclust@6.1.2 r-ggplot2@4.0.2 r-genomicranges@1.62.1 r-genomicfeatures@1.62.0 r-biostrings@2.78.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://github.com/almeidasilvaf/doubletrouble
Licenses: GPL 3
Build system: r
Synopsis: Identification and classification of duplicated genes
Description:

doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a simpler classification scheme, duplicates can also be classified into SD- and SSD-derived (small-scale duplication) gene pairs. Besides classifying gene pairs, users can also classify genes, so that each gene is assigned a unique mode of duplication. Users can also calculate substitution rates per substitution site (i.e., Ka and Ks) from duplicate pairs, find peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classify gene pairs into age groups based on Ks peaks.

r-deedeeexperiment 1.2.0
Propagated dependencies: r-writexl@1.5.4 r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-limma@3.66.0 r-edger@4.8.2 r-deseq2@1.50.2 r-cli@3.6.5
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://github.com/imbeimainz/DeeDeeExperiment
Licenses: Expat
Build system: r
Synopsis: DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results
Description:

DeeDeeExperiment is an S4 class extending the SingleCellExperiment class, designed to integrate and manage omics analysis results. It introduces two dedicated slots to store Differential Expression Analysis (DEA) results and Functional Enrichment Analysis (FEA) results, providing a structured approach for downstream analysis.

r-deltagseg 1.52.0
Propagated dependencies: r-wavethresh@4.7.3 r-tseries@0.10-60 r-scales@1.4.0 r-reshape@0.8.10 r-pvclust@2.2-0 r-ggplot2@4.0.2 r-fbasics@4052.98 r-changepoint@2.3
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/deltaGseg
Licenses: GPL 2
Build system: r
Synopsis: deltaGseg
Description:

Identifying distinct subpopulations through multiscale time series analysis.

r-dresscheck 0.50.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/dressCheck
Licenses: Artistic License 2.0
Build system: r
Synopsis: data and software for checking Dressman JCO 25(5) 2007
Description:

data and software for checking Dressman JCO 25(5) 2007.

r-drugvsdisease 2.54.0
Propagated dependencies: r-xtable@1.8-8 r-runit@0.4.33.1 r-qvalue@2.42.0 r-limma@3.66.0 r-hgu133plus2-db@3.13.0 r-hgu133a2-db@3.13.0 r-hgu133a-db@3.13.0 r-geoquery@2.78.0 r-drugvsdiseasedata@1.48.0 r-cmap2data@1.48.0 r-biomart@2.66.1 r-biocgenerics@0.56.0 r-arrayexpress@1.70.0 r-annotate@1.88.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DrugVsDisease
Licenses: GPL 3
Build system: r
Synopsis: Comparison of disease and drug profiles using Gene set Enrichment Analysis
Description:

This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Network visualisation of significant scores are output in Cytoscape format.

Page: 12122232425126
Total packages: 3017