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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-scarray-sat 1.9.0
Propagated dependencies: r-summarizedexperiment@1.38.1 r-seuratobject@5.1.0 r-seurat@5.3.0 r-scarray@1.18.0 r-s4vectors@0.46.0 r-matrix@1.7-3 r-gdsfmt@1.44.0 r-delayedarray@0.34.1 r-biocsingular@1.24.0 r-biocparallel@1.42.0 r-biocgenerics@0.54.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SCArray.sat
Licenses: GPL 3
Synopsis: Large-scale single-cell RNA-seq data analysis using GDS files and Seurat
Description:

Extends the Seurat classes and functions to support Genomic Data Structure (GDS) files as a DelayedArray backend for data representation. It relies on the implementation of GDS-based DelayedMatrix in the SCArray package to represent single cell RNA-seq data. The common optimized algorithms leveraging GDS-based and single cell-specific DelayedMatrix (SC_GDSMatrix) are implemented in the SCArray package. SCArray.sat introduces a new SCArrayAssay class (derived from the Seurat Assay), which wraps raw counts, normalized expressions and scaled data matrix based on GDS-specific DelayedMatrix. It is designed to integrate seamlessly with the Seurat package to provide common data analysis in the SeuratObject-based workflow. Compared with Seurat, SCArray.sat significantly reduces the memory usage without downsampling and can be applied to very large datasets.

r-scp 1.20.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://UCLouvain-CBIO.github.io/scp
Licenses: Artistic License 2.0
Synopsis: Mass Spectrometry-Based Single-Cell Proteomics Data Analysis
Description:

Utility functions for manipulating, processing, and analyzing mass spectrometry-based single-cell proteomics data. The package is an extension to the QFeatures package and relies on SingleCellExpirement to enable single-cell proteomics analyses. The package offers the user the functionality to process quantitative table (as generated by MaxQuant, Proteome Discoverer, and more) into data tables ready for downstream analysis and data visualization.

r-splicewiz 1.12.0
Dependencies: zlib@1.3.1
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/alexchwong/SpliceWiz
Licenses: Expat
Synopsis: interactive analysis and visualization of alternative splicing in R
Description:

The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across conditions. SpliceWiz features a shiny-based GUI facilitating interactive data exploration of results including gene ontology enrichment. It is performance optimized with multi-threaded processing of BAM files and a new COV file format for fast recall of sequencing coverage. Overall, SpliceWiz streamlines AS analysis, enabling reliable identification of functionally relevant AS events for further characterization.

r-seventygenedata 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/release/data/experiment/html/seventyGeneData.html
Licenses: Artistic License 2.0
Synopsis: ExpressionSets from the van't Veer and Van de Vijver breast cancer studies
Description:

Gene expression data for the two breast cancer cohorts published by van't Veer and Van de Vijver in 2002.

r-svm2crmdata 1.42.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SVM2CRMdata
Licenses: LGPL 2.0+
Synopsis: An example dataset for use with the SVM2CRM package
Description:

An example dataset for use with the SVM2CRM package.

r-systempipetools 1.18.0
Propagated dependencies: r-tibble@3.2.1 r-summarizedexperiment@1.38.1 r-rtsne@0.17 r-plotly@4.10.4 r-pheatmap@1.0.12 r-magrittr@2.0.3 r-glmpca@0.2.0 r-ggtree@3.16.0 r-ggrepel@0.9.6 r-ggplot2@3.5.2 r-ggally@2.2.1 r-dt@0.33 r-dplyr@1.1.4 r-deseq2@1.48.1 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/systemPipeTools
Licenses: Artistic License 2.0
Synopsis: Tools for data visualization
Description:

systemPipeTools package extends the widely used systemPipeR (SPR) workflow environment with an enhanced toolkit for data visualization, including utilities to automate the data visualizaton for analysis of differentially expressed genes (DEGs). systemPipeTools provides data transformation and data exploration functions via scatterplots, hierarchical clustering heatMaps, principal component analysis, multidimensional scaling, generalized principal components, t-Distributed Stochastic Neighbor embedding (t-SNE), and MA and volcano plots. All these utilities can be integrated with the modular design of the systemPipeR environment that allows users to easily substitute any of these features and/or custom with alternatives.

r-schex 1.24.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/SaskiaFreytag/schex
Licenses: GPL 3
Synopsis: Hexbin plots for single cell omics data
Description:

Builds hexbin plots for variables and dimension reduction stored in single cell omics data such as SingleCellExperiment. The ideas used in this package are based on the excellent work of Dan Carr, Nicholas Lewin-Koh, Martin Maechler and Thomas Lumley.

r-slqpcr 1.76.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SLqPCR
Licenses: GPL 2+
Synopsis: Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH
Description:

This package provides functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH.

r-synergyfinder 3.18.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: http://www.synergyfinder.org
Licenses: FSDG-compatible
Synopsis: Calculate and Visualize Synergy Scores for Drug Combinations
Description:

Efficient implementations for analyzing pre-clinical multiple drug combination datasets. It provides efficient implementations for 1.the popular synergy scoring models, including HSA, Loewe, Bliss, and ZIP to quantify the degree of drug combination synergy; 2. higher order drug combination data analysis and synergy landscape visualization for unlimited number of drugs in a combination; 3. statistical analysis of drug combination synergy and sensitivity with confidence intervals and p-values; 4. synergy barometer for harmonizing multiple synergy scoring methods to provide a consensus metric of synergy; 5. evaluation of synergy and sensitivity simultaneously to provide an unbiased interpretation of the clinical potential of the drug combinations. Based on this package, we also provide a web application (http://www.synergyfinder.org) for users who prefer graphical user interface.

r-sctgif 1.24.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/scTGIF
Licenses: Artistic License 2.0
Synopsis: Cell type annotation for unannotated single-cell RNA-Seq data
Description:

scTGIF connects the cells and the related gene functions without cell type label.

r-scshapes 1.16.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/Malindrie/scShapes
Licenses: GPL 3
Synopsis: Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data
Description:

We present a novel statistical framework for identifying differential distributions in single-cell RNA-sequencing (scRNA-seq) data between treatment conditions by modeling gene expression read counts using generalized linear models (GLMs). We model each gene independently under each treatment condition using error distributions Poisson (P), Negative Binomial (NB), Zero-inflated Poisson (ZIP) and Zero-inflated Negative Binomial (ZINB) with log link function and model based normalization for differences in sequencing depth. Since all four distributions considered in our framework belong to the same family of distributions, we first perform a Kolmogorov-Smirnov (KS) test to select genes belonging to the family of ZINB distributions. Genes passing the KS test will be then modeled using GLMs. Model selection is done by calculating the Bayesian Information Criterion (BIC) and likelihood ratio test (LRT) statistic.

r-scthi-data 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/scTHI.data
Licenses: GPL 2
Synopsis: The package contains examples of single cell data used in vignettes and examples of the scTHI package; data contain both tumor cells and immune cells from public dataset of glioma
Description:

Data for the vignette and tutorial of the package scTHI.

r-shinyepico 1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/omorante/shiny_epico
Licenses: FSDG-compatible
Synopsis: ShinyÉPICo
Description:

ShinyÉPICo is a graphical pipeline to analyze Illumina DNA methylation arrays (450k or EPIC). It allows to calculate differentially methylated positions and differentially methylated regions in a user-friendly interface. Moreover, it includes several options to export the results and obtain files to perform downstream analysis.

r-simffpe 1.22.0
Propagated dependencies: r-truncnorm@1.0-9 r-rsamtools@2.24.0 r-iranges@2.42.0 r-genomicranges@1.60.0 r-foreach@1.5.2 r-dplyr@1.1.4 r-doparallel@1.0.17 r-biostrings@2.76.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SimFFPE
Licenses: LGPL 3
Synopsis: NGS Read Simulator for FFPE Tissue
Description:

The NGS (Next-Generation Sequencing) reads from FFPE (Formalin-Fixed Paraffin-Embedded) samples contain numerous artifact chimeric reads (ACRS), which can lead to false positive structural variant calls. These ACRs are derived from the combination of two single-stranded DNA (ss-DNA) fragments with short reverse complementary regions (SRCRs). This package simulates these artifact chimeric reads as well as normal reads for FFPE samples on the whole genome / several chromosomes / large regions.

r-splinedv 1.2.0
Propagated dependencies: r-summarizedexperiment@1.38.1 r-sparsematrixstats@1.20.0 r-singlecellexperiment@1.30.1 r-scuttle@1.18.0 r-s4vectors@0.46.0 r-plotly@4.10.4 r-matrix@1.7-3 r-dplyr@1.1.4 r-biocgenerics@0.54.0 r-biobase@2.68.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/Xenon8778/SplineDV
Licenses: GPL 2
Synopsis: Differential Variability (DV) analysis for single-cell RNA sequencing data. (e.g. Identify Differentially Variable Genes across two experimental conditions)
Description:

This package provides a spline based scRNA-seq method for identifying differentially variable (DV) genes across two experimental conditions. Spline-DV constructs a 3D spline from 3 key gene statistics: mean expression, coefficient of variance, and dropout rate. This is done for both conditions. The 3D spline provides the “expected” behavior of genes in each condition. The distance of the observed mean, CV and dropout rate of each gene from the expected 3D spline is used to measure variability. As the final step, the spline-DV method compares the variabilities of each condition to identify differentially variable (DV) genes.

r-summix 2.16.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/Summix
Licenses: Expat
Synopsis: Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data
Description:

This package contains the Summix2 method for estimating and adjusting for substructure in genetic summary allele frequency data. The function summix() estimates reference group proportions using a mixture model. The adjAF() function produces adjusted allele frequencies for an observed group with reference group proportions matching a target individual or sample. The summix_local() function estimates local ancestry mixture proportions and performs selection scans in genetic summary data.

r-stabmap 1.4.0
Propagated dependencies: r-summarizedexperiment@1.38.1 r-slam@0.1-55 r-matrixgenerics@1.20.0 r-matrix@1.7-3 r-mass@7.3-65 r-igraph@2.1.4 r-biocsingular@1.24.0 r-biocparallel@1.42.0 r-biocneighbors@2.2.0 r-biocgenerics@0.54.0 r-abind@1.4-8
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://sydneybiox.github.io/StabMap
Licenses: GPL 2
Synopsis: Stabilised mosaic single cell data integration using unshared features
Description:

StabMap performs single cell mosaic data integration by first building a mosaic data topology, and for each reference dataset, traverses the topology to project and predict data onto a common embedding. Mosaic data should be provided in a list format, with all relevant features included in the data matrices within each list object. The output of stabMap is a joint low-dimensional embedding taking into account all available relevant features. Expression imputation can also be performed using the StabMap embedding and any of the original data matrices for given reference and query cell lists.

r-spotlight 1.14.0
Propagated dependencies: r-sparsematrixstats@1.20.0 r-singlecellexperiment@1.30.1 r-rcppeigen@0.3.4.0.2 r-rcpp@1.0.14 r-matrix@1.7-3 r-ggplot2@3.5.2
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/MarcElosua/SPOTlight
Licenses: GPL 3
Synopsis: `SPOTlight`: Spatial Transcriptomics Deconvolution
Description:

`SPOTlight` provides a method to deconvolute spatial transcriptomics spots using a seeded NMF approach along with visualization tools to assess the results. Spatially resolved gene expression profiles are key to understand tissue organization and function. However, novel spatial transcriptomics (ST) profiling techniques lack single-cell resolution and require a combination with single-cell RNA sequencing (scRNA-seq) information to deconvolute the spatially indexed datasets. Leveraging the strengths of both data types, we developed SPOTlight, a computational tool that enables the integration of ST with scRNA-seq data to infer the location of cell types and states within a complex tissue. SPOTlight is centered around a seeded non-negative matrix factorization (NMF) regression, initialized using cell-type marker genes and non-negative least squares (NNLS) to subsequently deconvolute ST capture locations (spots).

r-seqcombo 1.32.0
Propagated dependencies: r-yulab-utils@0.2.0 r-igraph@2.1.4 r-ggplot2@3.5.2
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/seqcombo
Licenses: Artistic License 2.0
Synopsis: Visualization Tool for Genetic Reassortment
Description:

This package provides useful functions for visualizing virus reassortment events.

r-simd 1.28.0
Propagated dependencies: r-statmod@1.5.0 r-methylmnm@1.48.0 r-edger@4.6.2
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SIMD
Licenses: GPL 3
Synopsis: Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site
Description:

This package provides a inferential analysis method for detecting differentially expressed CpG sites in MeDIP-seq data. It uses statistical framework and EM algorithm, to identify differentially expressed CpG sites. The methods on this package are described in the article Methylation-level Inferences and Detection of Differential Methylation with Medip-seq Data by Yan Zhou, Jiadi Zhu, Mingtao Zhao, Baoxue Zhang, Chunfu Jiang and Xiyan Yang (2018, pending publication).

r-synaptome-db 0.99.17
Propagated dependencies: r-synaptome-data@0.99.6 r-rsqlite@2.3.11 r-rdpack@2.6.4 r-igraph@2.1.4 r-dplyr@1.1.4 r-dbplyr@2.5.0 r-dbi@1.2.3 r-annotationhub@3.16.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/synaptome.db
Licenses: Artistic License 2.0
Synopsis: Synamptosome Proteome Database
Description:

The package contains local copy of the Synaptic proteome database. On top of this it provide a set of utility R functions to query and analyse its content. It allows extraction of information for specific genes and building the protein-protein interaction graph for gene sets, synaptic compartments, and brain regions.

r-sparrow 1.16.0
Propagated dependencies: r-viridis@0.6.5 r-plotly@4.10.4 r-matrix@1.7-3 r-limma@3.64.1 r-irlba@2.3.5.1 r-gseabase@1.70.0 r-ggplot2@3.5.2 r-edger@4.6.2 r-delayedmatrixstats@1.30.0 r-data-table@1.17.4 r-complexheatmap@2.24.0 r-circlize@0.4.16 r-checkmate@2.3.2 r-biocset@1.22.0 r-biocparallel@1.42.0 r-biocgenerics@0.54.0 r-babelgene@22.9
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/lianos/sparrow
Licenses: Expat
Synopsis: Take command of set enrichment analyses through a unified interface
Description:

This package provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.

r-screclassify 1.16.0
Propagated dependencies: r-summarizedexperiment@1.38.1 r-singlecellexperiment@1.30.1 r-randomforest@4.7-1.2 r-e1071@1.7-16
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/SydneyBioX/scReClassify
Licenses: FSDG-compatible
Synopsis: scReClassify: post hoc cell type classification of single-cell RNA-seq data
Description:

This package provides a post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique. The current version of scReClassify supports Support Vector Machine and Random Forest as a base classifier.

r-sradb 1.72.0
Propagated dependencies: r-rsqlite@2.3.11 r-rcurl@1.98-1.17 r-r-utils@2.13.0 r-graph@1.86.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SRAdb
Licenses: Artistic License 2.0
Synopsis: compilation of metadata from NCBI SRA and tools
Description:

The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.

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Total results: 45109