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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:

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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-splicingfactory 1.18.0
Propagated dependencies: r-summarizedexperiment@1.38.1
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/esebesty/SplicingFactory
Licenses: FSDG-compatible
Synopsis: Splicing Diversity Analysis for Transcriptome Data
Description:

The SplicingFactory R package uses transcript-level expression values to analyze splicing diversity based on various statistical measures, like Shannon entropy or the Gini index. These measures can quantify transcript isoform diversity within samples or between conditions. Additionally, the package analyzes the isoform diversity data, looking for significant changes between conditions.

r-speckle 1.10.0
Propagated dependencies: r-singlecellexperiment@1.30.1 r-seurat@5.3.0 r-limma@3.64.1 r-ggplot2@3.5.2 r-edger@4.6.2
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/speckle
Licenses: GPL 3
Synopsis: Statistical methods for analysing single cell RNA-seq data
Description:

The speckle package contains functions for the analysis of single cell RNA-seq data. The speckle package currently contains functions to analyse differences in cell type proportions. There are also functions to estimate the parameters of the Beta distribution based on a given counts matrix, and a function to normalise a counts matrix to the median library size. There are plotting functions to visualise cell type proportions and the mean-variance relationship in cell type proportions and counts. As our research into specialised analyses of single cell data continues we anticipate that the package will be updated with new functions.

r-spaniel 1.24.0
Propagated dependencies: r-summarizedexperiment@1.38.1 r-singlecellexperiment@1.30.1 r-shiny@1.10.0 r-seurat@5.3.0 r-scran@1.36.0 r-scater@1.36.0 r-s4vectors@0.46.0 r-png@0.1-8 r-magrittr@2.0.3 r-jsonlite@2.0.0 r-jpeg@0.1-11 r-igraph@2.1.4 r-ggplot2@3.5.2 r-dropletutils@1.28.0 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/Spaniel
Licenses: Expat
Synopsis: Spatial Transcriptomics Analysis
Description:

Spaniel includes a series of tools to aid the quality control and analysis of Spatial Transcriptomics data. Spaniel can import data from either the original Spatial Transcriptomics system or 10X Visium technology. The package contains functions to create a SingleCellExperiment Seurat object and provides a method of loading a histologial image into R. The spanielPlot function allows visualisation of metrics contained within the S4 object overlaid onto the image of the tissue.

r-spasim 1.12.0
Propagated dependencies: r-summarizedexperiment@1.38.1 r-spatstat-random@3.4-1 r-spatstat-geom@3.4-1 r-spatialexperiment@1.18.1 r-rann@2.6.2 r-ggplot2@3.5.2 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://trigosteam.github.io/spaSim/
Licenses: Artistic License 2.0
Synopsis: Spatial point data simulator for tissue images
Description:

This package provides a suite of functions for simulating spatial patterns of cells in tissue images. Output images are multitype point data in SingleCellExperiment format. Each point represents a cell, with its 2D locations and cell type. Potential cell patterns include background cells, tumour/immune cell clusters, immune rings, and blood/lymphatic vessels.

r-scmet 1.12.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/scMET
Licenses: GPL 3
Synopsis: Bayesian modelling of cell-to-cell DNA methylation heterogeneity
Description:

High-throughput single-cell measurements of DNA methylomes can quantify methylation heterogeneity and uncover its role in gene regulation. However, technical limitations and sparse coverage can preclude this task. scMET is a hierarchical Bayesian model which overcomes sparsity, sharing information across cells and genomic features to robustly quantify genuine biological heterogeneity. scMET can identify highly variable features that drive epigenetic heterogeneity, and perform differential methylation and variability analyses. We illustrate how scMET facilitates the characterization of epigenetically distinct cell populations and how it enables the formulation of novel hypotheses on the epigenetic regulation of gene expression.

r-sspaths 1.24.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/ssPATHS
Licenses: Expat
Synopsis: ssPATHS: Single Sample PATHway Score
Description:

This package generates pathway scores from expression data for single samples after training on a reference cohort. The score is generated by taking the expression of a gene set (pathway) from a reference cohort and performing linear discriminant analysis to distinguish samples in the cohort that have the pathway augmented and not. The separating hyperplane is then used to score new samples.

r-svmdo 1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SVMDO
Licenses: GPL 3
Synopsis: Identification of Tumor-Discriminating mRNA Signatures via Support Vector Machines Supported by Disease Ontology
Description:

It is an easy-to-use GUI using disease information for detecting tumor/normal sample discriminating gene sets from differentially expressed genes. Our approach is based on an iterative algorithm filtering genes with disease ontology enrichment analysis and wilk and wilks lambda criterion connected to SVM classification model construction. Along with gene set extraction, SVMDO also provides individual prognostic marker detection. The algorithm is designed for FPKM and RPKM normalized RNA-Seq transcriptome datasets.

r-switchbox 1.46.0
Propagated dependencies: r-proc@1.18.5 r-gplots@3.2.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/switchBox
Licenses: GPL 2
Synopsis: Utilities to train and validate classifiers based on pair switching using the K-Top-Scoring-Pair (KTSP) algorithm
Description:

The package offer different classifiers based on comparisons of pair of features (TSP), using various decision rules (e.g., majority wins principle).

r-spacemarkers 2.0.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/DeshpandeLab/SpaceMarkers
Licenses: Expat
Synopsis: Spatial Interaction Markers
Description:

Spatial transcriptomic technologies have helped to resolve the connection between gene expression and the 2D orientation of tissues relative to each other. However, the limited single-cell resolution makes it difficult to highlight the most important molecular interactions in these tissues. SpaceMarkers, R/Bioconductor software, can help to find molecular interactions, by identifying genes associated with latent space interactions in spatial transcriptomics.

r-serumstimulation 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/serumStimulation
Licenses: GPL 2+
Synopsis: serumStimulation is a data package which is used by examples in package pcaGoPromoter
Description:

This package contains 13 micro array data results from a serum stimulation experiment.

r-scgps 1.24.0
Propagated dependencies: r-summarizedexperiment@1.38.1 r-singlecellexperiment@1.30.1 r-rcppparallel@5.1.10 r-rcpparmadillo@14.4.3-1 r-rcpp@1.0.14 r-locfit@1.5-9.12 r-glmnet@4.1-8 r-ggplot2@3.5.2 r-fastcluster@1.3.0 r-dynamictreecut@1.63-1 r-dplyr@1.1.4 r-deseq2@1.48.1 r-caret@7.0-1
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/scGPS
Licenses: GPL 3
Synopsis: complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)
Description:

The package implements two main algorithms to answer two key questions: a SCORE (Stable Clustering at Optimal REsolution) to find subpopulations, followed by scGPS to investigate the relationships between subpopulations.

r-targetscore 1.48.0
Propagated dependencies: r-pracma@2.4.4 r-matrix@1.7-3
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: http://www.cs.utoronto.ca/~yueli/software.html
Licenses: GPL 2
Synopsis: TargetScore: Infer microRNA targets using microRNA-overexpression data and sequence information
Description:

Infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variaitonal Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final targetScore is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features.

r-triplex 1.50.0
Propagated dependencies: r-xvector@0.48.0 r-s4vectors@0.46.0 r-iranges@2.42.0 r-genomicranges@1.60.0 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: http://www.fi.muni.cz/~lexa/triplex/
Licenses: FreeBSD
Synopsis: Search and visualize intramolecular triplex-forming sequences in DNA
Description:

This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.

r-txdb-rnorvegicus-ucsc-rn7-refgene 3.15.0
Propagated dependencies: r-genomicfeatures@1.60.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Rnorvegicus.UCSC.rn7.refGene
Licenses: Artistic License 2.0
Synopsis: Annotation package for TxDb object(s)
Description:

Exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

r-tidyomics 1.6.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/tidyomics/tidyomics
Licenses: Expat
Synopsis: Easily install and load the tidyomics ecosystem
Description:

The tidyomics ecosystem is a set of packages for ’omic data analysis that work together in harmony; they share common data representations and API design, consistent with the tidyverse ecosystem. The tidyomics package is designed to make it easy to install and load core packages from the tidyomics ecosystem with a single command.

r-tvtb 1.36.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/kevinrue/TVTB
Licenses: Artistic License 2.0
Synopsis: TVTB: The VCF Tool Box
Description:

The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).

r-tpp2d 1.26.0
Propagated dependencies: r-tidyr@1.3.1 r-stringr@1.5.1 r-rcurl@1.98-1.17 r-openxlsx@4.2.8 r-mass@7.3-65 r-limma@3.64.1 r-ggplot2@3.5.2 r-foreach@1.5.2 r-dplyr@1.1.4 r-doparallel@1.0.17 r-biocparallel@1.42.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: http://bioconductor.org/packages/TPP2D
Licenses: GPL 3
Synopsis: Detection of ligand-protein interactions from 2D thermal profiles (DLPTP)
Description:

Detection of ligand-protein interactions from 2D thermal profiles (DLPTP), Performs an FDR-controlled analysis of 2D-TPP experiments by functional analysis of dose-response curves across temperatures.

r-txdb-rnorvegicus-ucsc-rn6-refgene 3.4.6
Propagated dependencies: r-genomicfeatures@1.60.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Rnorvegicus.UCSC.rn6.refGene
Licenses: Artistic License 2.0
Synopsis: Annotation package for TxDb object(s)
Description:

Exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

r-tfhaz 1.32.0
Propagated dependencies: r-s4vectors@0.46.0 r-orfik@1.30.1 r-iranges@2.42.0 r-genomicranges@1.60.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TFHAZ
Licenses: Artistic License 2.0
Synopsis: Transcription Factor High Accumulation Zones
Description:

It finds trascription factor (TF) high accumulation DNA zones, i.e., regions along the genome where there is a high presence of different transcription factors. Starting from a dataset containing the genomic positions of TF binding regions, for each base of the selected chromosome the accumulation of TFs is computed. Three different types of accumulation (TF, region and base accumulation) are available, together with the possibility of considering, in the single base accumulation computing, the TFs present not only in that single base, but also in its neighborhood, within a window of a given width. Two different methods for the search of TF high accumulation DNA zones, called "binding regions" and "overlaps", are available. In addition, some functions are provided in order to analyze, visualize and compare results obtained with different input parameters.

r-txdb-athaliana-biomart-plantsmart25 3.1.3
Propagated dependencies: r-genomicfeatures@1.60.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Athaliana.BioMart.plantsmart25
Licenses: Artistic License 2.0
Synopsis: Annotation package for TxDb object(s)
Description:

Exposes an annotation databases generated from BioMart by exposing these as TxDb objects.

r-tomoseqr 1.14.0
Propagated dependencies: r-tibble@3.2.1 r-stringr@1.5.1 r-shiny@1.10.0 r-readr@2.1.5 r-purrr@1.0.4 r-plotly@4.10.4 r-ggplot2@3.5.2 r-dplyr@1.1.4 r-biocfilecache@2.16.0 r-animation@2.7
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/tomoseqr
Licenses: Expat
Synopsis: R Package for Analyzing Tomo-seq Data
Description:

`tomoseqr` is an R package for analyzing Tomo-seq data. Tomo-seq is a genome-wide RNA tomography method that combines combining high-throughput RNA sequencing with cryosectioning for spatially resolved transcriptomics. `tomoseqr` reconstructs 3D expression patterns from tomo-seq data and visualizes the reconstructed 3D expression patterns.

r-txdb-ptroglodytes-ucsc-pantro6-refgene 3.10.0
Propagated dependencies: r-genomicfeatures@1.60.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Ptroglodytes.UCSC.panTro6.refGene
Licenses: Artistic License 2.0
Synopsis: Annotation package for TxDb object(s)
Description:

Exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

r-transcriptogramer 1.32.0
Propagated dependencies: r-topgo@2.59.0 r-tidyr@1.3.1 r-snow@0.4-4 r-reder@3.6.0 r-progress@1.2.3 r-limma@3.64.1 r-igraph@2.1.4 r-ggplot2@3.5.2 r-foreach@1.5.2 r-dosnow@1.0.20 r-data-table@1.17.4 r-biomart@2.64.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://github.com/arthurvinx/transcriptogramer
Licenses: GPL 2+
Synopsis: Transcriptional analysis based on transcriptograms
Description:

R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are, hence, genome wide gene expression profiles that provide a global view for the cellular metabolism, while indicating gene sets whose expressions are altered.

r-txdb-sscrofa-ucsc-susscr11-refgene 3.12.0
Propagated dependencies: r-genomicfeatures@1.60.0 r-annotationdbi@1.70.0
Channel: guix-bioc
Location: guix-bioc/packages/t.scm (guix-bioc packages t)
Home page: https://bioconductor.org/packages/TxDb.Sscrofa.UCSC.susScr11.refGene
Licenses: Artistic License 2.0
Synopsis: Annotation package for TxDb object(s)
Description:

Exposes an annotation databases generated from UCSC by exposing these as TxDb objects.

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Total results: 45109