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

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-sigsquared 1.42.0
Propagated dependencies: r-survival@3.8-3 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/sigsquared
Licenses: FSDG-compatible
Build system: r
Synopsis: Gene signature generation for functionally validated signaling pathways
Description:

By leveraging statistical properties (log-rank test for survival) of patient cohorts defined by binary thresholds, poor-prognosis patients are identified by the sigsquared package via optimization over a cost function reducing type I and II error.

r-snadata 1.56.0
Propagated dependencies: r-graph@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SNAData
Licenses: LGPL 2.0+
Build system: r
Synopsis: Social Networks Analysis Data Examples
Description:

Data from Wasserman & Faust (1999) "Social Network Analysis".

r-smartphos 1.0.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://lu-group-ukhd.github.io/SmartPhos/
Licenses: GPL 3
Build system: r
Synopsis: phosphoproteomics data analysis package with an interactive ShinyApp
Description:

To facilitate and streamline phosphoproteomics data analysis, we developed SmartPhos, an R package for the pre-processing, quality control, and exploratory analysis of phosphoproteomics data generated by MaxQuant and Spectronaut. The package can be used either through the R command line or through an interactive ShinyApp called SmartPhos Explorer. The package contains methods such as normalization and normalization correction, transformation, imputation, batch effect correction, PCA, heatmap, differential expression, time-series clustering, gene set enrichment analysis, and kinase activity inference.

r-seq-hotspot 1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/sydney-grant/seq.hotSPOT
Licenses: Artistic License 2.0
Build system: r
Synopsis: Targeted sequencing panel design based on mutation hotspots
Description:

seq.hotSPOT provides a resource for designing effective sequencing panels to help improve mutation capture efficacy for ultradeep sequencing projects. Using SNV datasets, this package designs custom panels for any tissue of interest and identify the genomic regions likely to contain the most mutations. Establishing efficient targeted sequencing panels can allow researchers to study mutation burden in tissues at high depth without the economic burden of whole-exome or whole-genome sequencing. This tool was developed to make high-depth sequencing panels to study low-frequency clonal mutations in clinically normal and cancerous tissues.

r-sim 1.80.0
Propagated dependencies: r-quantsmooth@1.76.0 r-quantreg@6.1 r-globaltest@5.64.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SIM
Licenses: GPL 2+
Build system: r
Synopsis: Integrated Analysis on two human genomic datasets
Description:

Finds associations between two human genomic datasets.

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
Build system: r
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-sccomp 2.2.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/MangiolaLaboratory/sccomp
Licenses: GPL 3
Build system: r
Synopsis: Differential Composition and Variability Analysis for Single-Cell Data
Description:

Comprehensive R package for differential composition and variability analysis in single-cell RNA sequencing, CyTOF, and microbiome data. Provides robust Bayesian modeling with outlier detection, random effects, and advanced statistical methods for cell type proportion analysis. Features include probabilistic outlier identification, mixed-effect modeling, differential variability testing, and comprehensive visualization tools. Perfect for cancer research, immunology, developmental biology, and single-cell genomics applications.

r-synlet 2.10.0
Propagated dependencies: r-rcolorbrewer@1.1-3 r-rankprod@3.36.0 r-patchwork@1.3.2 r-magrittr@2.0.4 r-ggplot2@4.0.1 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/synlet
Licenses: GPL 3
Build system: r
Synopsis: Hits Selection for Synthetic Lethal RNAi Screen Data
Description:

Select hits from synthetic lethal RNAi screen data. For example, there are two identical celllines except one gene is knocked-down in one cellline. The interest is to find genes that lead to stronger lethal effect when they are knocked-down further by siRNA. Quality control and various visualisation tools are implemented. Four different algorithms could be used to pick up the interesting hits. This package is designed based on 384 wells plates, but may apply to other platforms with proper configuration.

r-sitepath 1.26.0
Propagated dependencies: r-tidytree@0.4.6 r-seqinr@4.2-36 r-rcpp@1.1.0 r-rcolorbrewer@1.1-3 r-gridextra@2.3 r-ggtree@4.0.1 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-aplot@0.2.9 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://wuaipinglab.github.io/sitePath/
Licenses: Expat
Build system: r
Synopsis: Phylogeny-based sequence clustering with site polymorphism
Description:

Using site polymorphism is one of the ways to cluster DNA/protein sequences but it is possible for the sequences with the same polymorphism on a single site to be genetically distant. This package is aimed at clustering sequences using site polymorphism and their corresponding phylogenetic trees. By considering their location on the tree, only the structurally adjacent sequences will be clustered. However, the adjacent sequences may not necessarily have the same polymorphism. So a branch-and-bound like algorithm is used to minimize the entropy representing the purity of site polymorphism of each cluster.

r-synapsis 1.16.0
Propagated dependencies: r-ebimage@4.52.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/synapsis
Licenses: Expat
Build system: r
Synopsis: An R package to automate the analysis of double-strand break repair during meiosis
Description:

Synapsis is a Bioconductor software package for automated (unbiased and reproducible) analysis of meiotic immunofluorescence datasets. The primary functions of the software can i) identify cells in meiotic prophase that are labelled by a synaptonemal complex axis or central element protein, ii) isolate individual synaptonemal complexes and measure their physical length, iii) quantify foci and co-localise them with synaptonemal complexes, iv) measure interference between synaptonemal complex-associated foci. The software has applications that extend to multiple species and to the analysis of other proteins that label meiotic prophase chromosomes. The software converts meiotic immunofluorescence images into R data frames that are compatible with machine learning methods. Given a set of microscopy images of meiotic spread slides, synapsis crops images around individual single cells, counts colocalising foci on strands on a per cell basis, and measures the distance between foci on any given strand.

r-suitor 1.12.0
Propagated dependencies: r-ggplot2@4.0.1 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/SUITOR
Licenses: GPL 2
Build system: r
Synopsis: Selecting the number of mutational signatures through cross-validation
Description:

An unsupervised cross-validation method to select the optimal number of mutational signatures. A data set of mutational counts is split into training and validation data.Signatures are estimated in the training data and then used to predict the mutations in the validation data.

r-scoreinvhap 1.32.0
Propagated dependencies: r-variantannotation@1.56.0 r-summarizedexperiment@1.40.0 r-snpstats@1.60.0 r-genomicranges@1.62.0 r-biostrings@2.78.0 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/scoreInvHap
Licenses: FSDG-compatible
Build system: r
Synopsis: Get inversion status in predefined regions
Description:

scoreInvHap can get the samples inversion status of known inversions. scoreInvHap uses SNP data as input and requires the following information about the inversion: genotype frequencies in the different haplotypes, R2 between the region SNPs and inversion status and heterozygote genotypes in the reference. The package include this data for 21 inversions.

r-screenr 1.12.1
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://emanuelsoda.github.io/ScreenR/
Licenses: Expat
Build system: r
Synopsis: Package to Perform High Throughput Biological Screening
Description:

ScreenR is a package suitable to perform hit identification in loss of function High Throughput Biological Screenings performed using barcoded shRNA-based libraries. ScreenR combines the computing power of software such as edgeR with the simplicity of use of the Tidyverse metapackage. ScreenR executes a pipeline able to find candidate hits from barcode counts, and integrates a wide range of visualization modes for each step of the analysis.

r-scnorm 1.32.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-quantreg@6.1 r-moments@0.14.1 r-ggplot2@4.0.1 r-forcats@1.0.1 r-data-table@1.17.8 r-cluster@2.1.8.1 r-biocparallel@1.44.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/rhondabacher/SCnorm
Licenses: GPL 2+
Build system: r
Synopsis: Normalization of single cell RNA-seq data
Description:

This package implements SCnorm — a method to normalize single-cell RNA-seq data.

r-stadyum 1.0.2
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/rhassett-cshl/STADyUM
Licenses: Expat
Build system: r
Synopsis: Statistical Transcriptome Analysis under a Dynamic Unified Model
Description:

STADyUM is a package with functionality for analyzing nascent RNA read counts to infer transcription rates. This includes utilities for processing experimental nascent RNA read counts as well as for simulating PRO-seq data. Rates such as initiation, pause release and landing pad occupancy are estimated from either synthetic or experimental data. There are also options for varying pause sites and including steric hindrance of initiation in the model.

r-scbfa 1.24.0
Propagated dependencies: r-zinbwave@1.32.0 r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-seurat@5.3.1 r-matrix@1.7-4 r-mass@7.3-65 r-ggplot2@4.0.1 r-deseq2@1.50.2 r-copula@1.1-7
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/ucdavis/quon-titative-biology/BFA
Licenses: FSDG-compatible
Build system: r
Synopsis: dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
Description:

This package is designed to model gene detection pattern of scRNA-seq through a binary factor analysis model. This model allows user to pass into a cell level covariate matrix X and gene level covariate matrix Q to account for nuisance variance(e.g batch effect), and it will output a low dimensional embedding matrix for downstream analysis.

r-safe 3.50.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/safe
Licenses: GPL 2+
Build system: r
Synopsis: Significance Analysis of Function and Expression
Description:

SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.

r-snageedata 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: http://fleming.ulb.ac.be/SNAGEE
Licenses: Artistic License 2.0
Build system: r
Synopsis: SNAGEE data
Description:

SNAGEE data - gene list and correlation matrix.

r-sparrow 1.16.0
Propagated dependencies: r-viridis@0.6.5 r-plotly@4.11.0 r-matrix@1.7-4 r-limma@3.66.0 r-irlba@2.3.5.1 r-gseabase@1.72.0 r-ggplot2@4.0.1 r-edger@4.8.0 r-delayedmatrixstats@1.32.0 r-data-table@1.17.8 r-complexheatmap@2.26.0 r-circlize@0.4.16 r-checkmate@2.3.3 r-biocset@1.24.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 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
Build system: r
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-sangeranalyser 1.20.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/sangeranalyseR
Licenses: GPL 2
Build system: r
Synopsis: sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
Description:

This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.

r-spasim 1.12.0
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
Build system: r
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-semisup 1.34.0
Propagated dependencies: r-vgam@1.1-13
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://github.com/rauschenberger/semisup
Licenses: GPL 3
Build system: r
Synopsis: Semi-Supervised Mixture Model
Description:

This package implements a parametric semi-supervised mixture model. The permutation test detects markers with main or interactive effects, without distinguishing them. Possible applications include genome-wide association analysis and differential expression analysis.

r-screcover 1.26.0
Propagated dependencies: r-saver@1.1.2 r-rsvd@1.0.5 r-pscl@1.5.9 r-preseqr@4.0.0 r-penalized@0.9-53 r-matrix@1.7-4 r-mass@7.3-65 r-kernlab@0.9-33 r-gamlss@5.5-0 r-foreach@1.5.2 r-doparallel@1.0.17 r-biocparallel@1.44.0 r-bbmle@1.0.25.1
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://miaozhun.github.io/scRecover
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: scRecover for imputation of single-cell RNA-seq data
Description:

scRecover is an R package for imputation of single-cell RNA-seq (scRNA-seq) data. It will detect and impute dropout values in a scRNA-seq raw read counts matrix while keeping the real zeros unchanged, since there are both dropout zeros and real zeros in scRNA-seq data. By combination with scImpute, SAVER and MAGIC, scRecover not only detects dropout and real zeros at higher accuracy, but also improve the downstream clustering and visualization results.

r-stategra 1.46.0
Propagated dependencies: r-mass@7.3-65 r-limma@3.66.0 r-gridextra@2.3 r-gplots@3.2.0 r-ggplot2@4.0.1 r-foreach@1.5.2 r-edger@4.8.0 r-calibrate@1.7.7 r-biobase@2.70.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/s.scm (guix-bioc packages s)
Home page: https://bioconductor.org/packages/STATegRa
Licenses: GPL 2
Build system: r
Synopsis: Classes and methods for multi-omics data integration
Description:

This package provides classes and tools for multi-omics data integration.

Total results: 2911