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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-methylumi 2.56.0
Propagated dependencies: r-annotate@1.88.0 r-annotationdbi@1.72.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-fdb-infiniummethylation-hg19@2.2.0 r-genefilter@1.92.0 r-genomeinfodb@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-illuminaio@0.52.0 r-iranges@2.44.0 r-lattice@0.22-7 r-matrixstats@1.5.0 r-minfi@1.56.0 r-reshape2@1.4.5 r-s4vectors@0.48.0 r-scales@1.4.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/methylumi
Licenses: GPL 2
Build system: r
Synopsis: Handle Illumina methylation data
Description:

This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.

r-illumina450probevariants-db 1.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Illumina450ProbeVariants.db
Licenses: GPL 3
Build system: r
Synopsis: Variant data from 1000 Genomes Project for Illumina HumanMethylation450 Bead Chip probes
Description:

This package includes details on variants for each probe on the 450k bead chip for each of the four populations (Asian, American, African and European).

r-yamss 1.36.0
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-ebimage@4.52.0 r-iranges@2.44.0 r-limma@3.66.0 r-matrix@1.7-4 r-mzr@2.44.0 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/hansenlab/yamss
Licenses: Artistic License 2.0
Build system: r
Synopsis: Tools for high-throughput metabolomics
Description:

This package provides tools to analyze and visualize high-throughput metabolomics data acquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.

r-microbiome 1.32.0
Propagated dependencies: r-biostrings@2.78.0 r-compositions@2.0-9 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-phyloseq@1.54.0 r-reshape2@1.4.5 r-rtsne@0.17 r-scales@1.4.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-vegan@2.7-2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://microbiome.github.io/microbiome/
Licenses: FreeBSD
Build system: r
Synopsis: Tools for microbiome analysis
Description:

This package facilitates phyloseq exploration and analysis of taxonomic profiling data. This package provides tools for the manipulation, statistical analysis, and visualization of taxonomic profiling data. In addition to targeted case-control studies, microbiome facilitates scalable exploration of population cohorts. This package supports the independent phyloseq data format and expands the available toolkit in order to facilitate the standardization of the analyses and the development of best practices.

r-italicsdata 2.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://bioinfo.curie.fr
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: ITALICS data
Description:

This package provides data needed to use the ITALICS package.

r-flowai 1.40.0
Propagated dependencies: r-changepoint@2.3 r-flowcore@2.22.0 r-ggplot2@4.0.1 r-knitr@1.50 r-plyr@1.8.9 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-rmarkdown@2.30 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/flowAI
Licenses: GPL 2+
Build system: r
Synopsis: Automatic and interactive quality control for flow cytometry data
Description:

This package is able to perform an automatic or interactive quality control on FCS data acquired using flow cytometry instruments. By evaluating three different properties:

  1. flow rate

  2. signal acquisition, and

  3. dynamic range,

the quality control enables the detection and removal of anomalies.

r-plgem 1.82.0
Propagated dependencies: r-biobase@2.70.0 r-mass@7.3-65
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.genopolis.it
Licenses: GPL 2
Build system: r
Synopsis: Detect differential expression in microarray and proteomics datasets
Description:

The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use of PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets.

r-beachmat 2.26.0
Propagated dependencies: r-assorthead@1.4.0 r-biocgenerics@0.56.0 r-delayedarray@0.36.0 r-matrix@1.7-4 r-rcpp@1.1.0 r-sparsearray@1.10.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/beachmat
Licenses: GPL 3
Build system: r
Synopsis: Compiling Bioconductor to handle each matrix type
Description:

This package provides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.

r-slingshot 2.18.0
Propagated dependencies: r-igraph@2.2.1 r-matrixstats@1.5.0 r-princurve@2.1.6 r-s4vectors@0.48.0 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0 r-trajectoryutils@1.18.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/slingshot
Licenses: Artistic License 2.0
Build system: r
Synopsis: Tools for ordering single-cell sequencing
Description:

This package provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.

r-lumi 2.62.0
Propagated dependencies: r-affy@1.88.0 r-annotate@1.88.0 r-annotationdbi@1.72.0 r-biobase@2.70.0 r-dbi@1.2.3 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-kernsmooth@2.23-26 r-lattice@0.22-7 r-mass@7.3-65 r-methylumi@2.56.0 r-mgcv@1.9-4 r-nleqslv@3.3.5 r-preprocesscore@1.72.0 r-rsqlite@2.4.4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/lumi
Licenses: LGPL 2.0+
Build system: r
Synopsis: BeadArray-specific methods for Illumina methylation and expression microarrays
Description:

The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.

r-copywriter 2.29.0
Propagated dependencies: r-biocparallel@1.44.0 r-chipseq@1.60.0 r-copyhelper@1.42.0 r-data-table@1.17.8 r-dnacopy@1.84.0 r-futile-logger@1.4.3 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-gtools@3.9.5 r-iranges@2.44.0 r-matrixstats@1.5.0 r-rsamtools@2.26.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/PeeperLab/CopywriteR
Licenses: GPL 2
Build system: r
Synopsis: Copy number information from targeted sequencing
Description:

CopywriteR extracts DNA copy number information from targeted sequencing by utilizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.

r-lpsymphony 1.38.0
Dependencies: zlib@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://r-forge.r-project.org/projects/rsymphony
Licenses: EPL 1.0
Build system: r
Synopsis: Symphony integer linear programming solver in R
Description:

This package was derived from Rsymphony. The package provides an R interface to SYMPHONY, a linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code, while Rsymphony expects to find header and library files on the users' system. Thus the intention of lpsymphony is to provide an easy to install interface to SYMPHONY.

r-bsgenome-hsapiens-ucsc-hg38-masked 1.4.5
Propagated dependencies: r-bsgenome@1.78.0 r-bsgenome-hsapiens-ucsc-hg38@1.4.5 r-genomeinfodb@1.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38.masked
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full masked genomic sequences for Homo sapiens (UCSC version hg38)
Description:

This package provides the complete genome sequences for Homo sapiens as provided by UCSC (genome hg38, based on assembly GRCh38.p14 since 2023/01/31). The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each of them has the 4 following masks on top:

  1. the mask of assembly gaps (AGAPS mask);

  2. the mask of intra-contig ambiguities (AMB mask);

  3. the mask of repeats from RepeatMasker (RM mask);

  4. the mask of repeats from Tandem Repeats Finder (TRF mask).

Only the AGAPS and AMB masks are "active" by default. The sequences are stored in MaskedDNAString objects.

r-screpertoire 2.5.8
Propagated dependencies: r-dplyr@1.1.4 r-evmix@2.12 r-ggalluvial@0.12.5 r-ggdendro@0.2.0 r-ggplot2@4.0.1 r-ggraph@2.2.2 r-igraph@2.2.1 r-immapex@1.4.0 r-inext@3.0.2 r-lifecycle@1.0.4 r-matrix@1.7-4 r-purrr@1.2.0 r-quantreg@6.1 r-rcpp@1.1.0 r-rjson@0.2.23 r-rlang@1.1.6 r-s4vectors@0.48.0 r-seuratobject@5.2.0 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0 r-tidygraph@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/scRepertoire
Licenses: GPL 2
Build system: r
Synopsis: Toolkit for single-cell immune receptor profiling
Description:

The scRepertoire package was built to process data derived from the 10x Genomics Chromium Immune Profiling for both TCR and Ig enrichment workflows and subsequently interacts with the popular Seurat and SingleCellExperiment R packages. It also allows for general analysis of single-cell clonotype information without the use of expression information. The package functions as a wrapper for Startrac and powerTCR R packages.

r-bsgenome-drerio-ucsc-danrer7 1.4.0
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer7
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Danio rerio (UCSC version danRer7)
Description:

This package provides full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects.

r-annotationfuncs 1.40.0
Propagated dependencies: r-annotationdbi@1.72.0 r-dbi@1.2.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.iysik.com/r/annotationfuncs
Licenses: GPL 2
Build system: r
Synopsis: Annotation translation functions
Description:

This package provides functions for handling translating between different identifieres using the Biocore Data Team data-packages (e.g. org.Bt.eg.db).

r-snpstats 1.60.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-biocgenerics@0.56.0 r-matrix@1.7-4 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/snpStats
Licenses: GPL 3
Build system: r
Synopsis: Methods for SNP association studies
Description:

This package provides classes and statistical methods for large single-nucleotide polymorphism (SNP) association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.

r-abarray 1.78.0
Propagated dependencies: r-biobase@2.70.0 r-multtest@2.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ABarray
Licenses: GPL 2+
Build system: r
Synopsis: Gene expression analysis for Applied Biosystems Genome Survey Microarray
Description:

The package ABarray is designed to work with Applied Biosystems whole genome microarray platform, as well as any other platform whose data can be transformed into expression data matrix. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A graphical user interface (GUI) is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used.

r-maaslin2 1.22.0
Propagated dependencies: r-biglm@0.9-3 r-car@3.1-3 r-chemometrics@1.4.4 r-cplm@0.7-12.1 r-data-table@1.17.8 r-dplyr@1.1.4 r-edger@4.8.0 r-ggplot2@4.0.1 r-glmmtmb@1.1.13 r-hash@2.2.6.3 r-lme4@1.1-37 r-lmertest@3.1-3 r-logging@0.10-108 r-mass@7.3-65 r-metagenomeseq@1.52.0 r-optparse@1.7.5 r-pbapply@1.7-4 r-pcapp@2.0-5 r-pheatmap@1.0.13 r-pscl@1.5.9 r-robustbase@0.99-6 r-tibble@3.3.0 r-vegan@2.7-2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://huttenhower.sph.harvard.edu/maaslin2
Licenses: Expat
Build system: r
Synopsis: Multivariable association discovery in population-scale meta-omics studies
Description:

MaAsLin2 is comprehensive R package for efficiently determining multivariable association between clinical metadata and microbial meta'omic features. This package relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods.

r-bbcanalyzer 1.40.0
Propagated dependencies: r-biostrings@2.78.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rsamtools@2.26.0 r-summarizedexperiment@1.40.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BBCAnalyzer
Licenses: LGPL 3
Build system: r
Synopsis: Visualizing base counts
Description:

BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.

r-rcas 1.36.0
Dependencies: pandoc@2.19.2
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-bsgenome@1.78.0 r-bsgenome-hsapiens-ucsc-hg19@1.4.3 r-cowplot@1.2.0 r-data-table@1.17.8 r-dt@0.34.0 r-genomation@1.42.0 r-genomeinfodb@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-gprofiler2@0.2.4 r-iranges@2.44.0 r-knitr@1.50 r-pbapply@1.7-4 r-pheatmap@1.0.13 r-plotly@4.11.0 r-plotrix@3.8-13 r-proxy@0.4-27 r-ranger@0.17.0 r-rmarkdown@2.30 r-rsqlite@2.4.4 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqlogo@1.76.0 r-txdbmaker@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/BIMSBbioinfo/RCAS
Licenses: Artistic License 2.0
Build system: r
Synopsis: RNA-centric annotation system
Description:

RCAS aims to be a standalone RNA-centric annotation system that provides intuitive reports and publication-ready graphics. This package provides the R library implementing most of the pipeline's features.

r-genomationdata 1.42.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioinformatics.mdc-berlin.de/genomation/
Licenses: GPL 3+
Build system: r
Synopsis: Experimental data for use with the genomation package
Description:

This package contains experimental genetic data for use with the genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.

r-debcam 1.26.0
Dependencies: openjdk@11.0.22 java-pj@20150107
Propagated dependencies: r-apcluster@1.4.14 r-biobase@2.70.0 r-biocparallel@1.44.0 r-corpcor@1.6.10 r-dmwr2@0.0.2 r-geometry@0.5.2 r-nmf@0.28 r-nnls@1.6 r-pcapp@2.0-5 r-rjava@1.0-11 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/debCAM
Licenses: GPL 2
Build system: r
Synopsis: Deconvolution by convex analysis of mixtures
Description:

This package is an R implementation for fully unsupervised deconvolution of complex tissues. DebCAM provides basic functions to perform unsupervised deconvolution on mixture expression profiles by CAM and some auxiliary functions to help understand the subpopulation- specific results. It also implements functions to perform supervised deconvolution based on prior knowledge of molecular markers, S matrix or A matrix. Combining molecular markers from CAM and from prior knowledge can achieve semi-supervised deconvolution of mixtures.

r-amplican 1.32.1
Propagated dependencies: r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biostrings@2.78.0 r-cluster@2.1.8.1 r-data-table@1.17.8 r-dplyr@1.1.4 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-ggthemes@5.1.0 r-gridextra@2.3 r-gtable@0.3.6 r-iranges@2.44.0 r-knitr@1.50 r-matrix@1.7-4 r-matrixstats@1.5.0 r-pwalign@1.6.0 r-rcpp@1.1.0 r-rmarkdown@2.30 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-shortread@1.68.0 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/valenlab/amplican
Licenses: GPL 3
Build system: r
Synopsis: Automated analysis of CRISPR experiments
Description:

The package performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents the results in the form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.

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Total results: 69112