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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-nbpseq 0.3.1
Propagated dependencies: r-qvalue@2.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/web/packages/NBPSeq
Licenses: GPL 2
Synopsis: Negative binomial models for RNA-Seq data
Description:

This package provides negative binomial models for two-group comparisons and regression inferences from RNA-sequencing data.

r-illuminahumanmethylationepicv2manifest 1.0.0
Propagated dependencies: r-minfi@1.54.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html
Licenses: Artistic License 2.0
Synopsis: Manifest for Illumina's EPIC v2.0 methylation arrays
Description:

This package provides a manifest package for Illumina's EPIC v2.0 methylation arrays. The version 2 covers more than 935K CpG sites in the human genome hg38. It is an update of the original EPIC v1.0 array (i.e., the 850K methylation array).

r-chippeakanno 3.42.0
Propagated dependencies: r-annotationdbi@1.70.0 r-biocgenerics@0.54.0 r-biomart@2.64.0 r-biostrings@2.76.0 r-data-table@1.17.4 r-dbi@1.2.3 r-dplyr@1.1.4 r-ensembldb@2.32.0 r-genomeinfodb@1.44.0 r-genomicalignments@1.44.0 r-genomicfeatures@1.60.0 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-graph@1.86.0 r-interactionset@1.36.1 r-iranges@2.42.0 r-keggrest@1.48.0 r-matrixstats@1.5.0 r-multtest@2.64.0 r-pwalign@1.4.0 r-rbgl@1.84.0 r-regioner@1.39.0 r-rsamtools@2.24.0 r-rtracklayer@1.68.0 r-s4vectors@0.46.0 r-scales@1.4.0 r-stringr@1.5.1 r-summarizedexperiment@1.38.1 r-tibble@3.2.1 r-tidyr@1.3.1 r-universalmotif@1.26.2 r-venndiagram@1.7.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ChIPpeakAnno
Licenses: GPL 2+
Synopsis: Peaks annotation from ChIP-seq and ChIP-chip experiments
Description:

The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs).

r-flowsorted-blood-epic 2.12.0
Propagated dependencies: r-annotationhub@3.16.0 r-experimenthub@2.16.0 r-genefilter@1.90.0 r-minfi@1.54.1 r-nlme@3.1-168 r-quadprog@1.5-8 r-s4vectors@0.46.0 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/immunomethylomics/FlowSorted.Blood.EPIC
Licenses: GPL 3
Synopsis: Illumina EPIC data on immunomagnetic sorted peripheral adult blood cells
Description:

This package provides raw data objects to be used for blood cell proportion estimation in minfi and similar packages. The FlowSorted.Blood.EPIC object is based in samples assayed by Brock Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554.

r-bisquerna 1.0.5
Propagated dependencies: r-biobase@2.68.0 r-limsolve@1.5.7.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.biorxiv.org/content/10.1101/669911v1
Licenses: GPL 3
Synopsis: Decomposition of bulk expression with single-cell sequencing
Description:

This package provides tools to accurately estimate cell type abundances from heterogeneous bulk expression. A reference-based method utilizes single-cell information to generate a signature matrix and transformation of bulk expression for accurate regression based estimates. A marker-based method utilizes known cell-specific marker genes to measure relative abundances across samples.

r-rtcga 1.38.0
Propagated dependencies: r-assertthat@0.2.1 r-data-table@1.17.4 r-dplyr@1.1.4 r-ggplot2@3.5.2 r-ggthemes@5.1.0 r-htmltools@0.5.8.1 r-knitr@1.50 r-purrr@1.0.4 r-rcurl@1.98-1.17 r-rmarkdown@2.29 r-rvest@1.0.5 r-scales@1.4.0 r-stringi@1.8.7 r-survival@3.8-3 r-survminer@0.5.0 r-viridis@0.6.5 r-xml@3.99-0.18 r-xml2@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://rtcga.github.io/RTCGA/
Licenses: GPL 2
Synopsis: The Cancer Genome Atlas data integration
Description:

The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.

r-msmseda 1.46.0
Propagated dependencies: r-gplots@3.2.0 r-mass@7.3-65 r-msnbase@2.34.1 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/msmsEDA
Licenses: GPL 2
Synopsis: Exploratory data analysis of LC-MS/MS data by spectral counts
Description:

Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.

r-wppi 1.16.0
Propagated dependencies: r-dplyr@1.1.4 r-igraph@2.1.4 r-logger@0.4.0 r-magrittr@2.0.3 r-matrix@1.7-3 r-omnipathr@3.14.0 r-progress@1.2.3 r-purrr@1.0.4 r-rcurl@1.98-1.17 r-rlang@1.1.6 r-tibble@3.2.1 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/AnaGalhoz37/wppi
Licenses: Expat
Synopsis: Weighting protein-protein interactions
Description:

This package predicts functional relevance of protein-protein interactions based on functional annotations such as Human Protein Ontology and Gene Ontology, and prioritizes genes based on network topology, functional scores and a path search algorithm.

r-biosigner 1.36.0
Propagated dependencies: r-biobase@2.68.0 r-e1071@1.7-16 r-multiassayexperiment@1.34.0 r-multidataset@1.36.0 r-randomforest@4.7-1.2 r-ropls@1.40.0 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/biosigner/
Licenses: CeCILL
Synopsis: Signature discovery from omics data
Description:

Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding 'restricted' models are returned, enabling future predictions on new datasets.

r-regioner 1.39.0
Propagated dependencies: r-biostrings@2.76.0 r-bsgenome@1.76.0 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-memoise@2.0.1 r-rtracklayer@1.68.0 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/regioneR/
Licenses: Artistic License 2.0
Synopsis: Association analysis of genomic regions
Description:

This package offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.

r-scry 1.20.0
Propagated dependencies: r-biocsingular@1.24.0 r-delayedarray@0.34.1 r-glmpca@0.2.0 r-matrix@1.7-3 r-singlecellexperiment@1.30.1 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/scry.html
Licenses: Artistic License 2.0
Synopsis: Small-count analysis methods for high-dimensional data
Description:

Many modern biological datasets consist of small counts that are not well fit by standard linear-Gaussian methods such as principal component analysis. This package provides implementations of count-based feature selection and dimension reduction algorithms. These methods can be used to facilitate unsupervised analysis of any high-dimensional data such as single-cell RNA-seq.

r-limma 3.64.1
Propagated dependencies: r-statmod@1.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioinf.wehi.edu.au/limma
Licenses: GPL 2+
Synopsis: Package for linear models for microarray and RNA-seq data
Description:

This package can be used for the analysis of gene expression studies, especially the use of linear models for analysing designed experiments and the assessment of differential expression. The analysis methods apply to different technologies, including microarrays, RNA-seq, and quantitative PCR.

r-deds 1.60.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/DEDS/
Licenses: LGPL 3+
Synopsis: Differential expression via distance summary for microarray data
Description:

This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.

r-alphabeta 1.22.0
Propagated dependencies: r-biocparallel@1.42.0 r-data-table@1.17.4 r-dplyr@1.1.4 r-expm@1.0-0 r-ggplot2@3.5.2 r-gtools@3.9.5 r-igraph@2.1.4 r-optimx@2025-4.9 r-plotly@4.10.4 r-stringr@1.5.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AlphaBeta
Licenses: GPL 3
Synopsis: Estimate epimutation rates and spectra from DNA methylations in plants
Description:

The package AlphaBeta is a computational method for estimating epimutation rates and spectra from high-throughput DNA methylation data in plants. The method has been specifically designed to:

  • analyze germline epimutations in the context of multi-generational mutation accumulation lines;

  • analyze somatic epimutations in the context of plant development and aging.

r-rsamtools 2.24.0
Propagated dependencies: r-biocgenerics@0.54.0 r-biocparallel@1.42.0 r-biostrings@2.76.0 r-bitops@1.0-9 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-rhtslib@3.4.0 r-s4vectors@0.46.0 r-xvector@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/release/bioc/html/Rsamtools.html
Licenses: Expat
Synopsis: Interface to samtools, bcftools, and tabix
Description:

This package provides an interface to the samtools, bcftools, and tabix utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

r-structstrings 1.24.0
Propagated dependencies: r-biocgenerics@0.54.0 r-biostrings@2.76.0 r-crayon@1.5.3 r-iranges@2.42.0 r-s4vectors@0.46.0 r-stringi@1.8.7 r-stringr@1.5.1 r-xvector@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/FelixErnst/Structstrings
Licenses: Artistic License 2.0
Synopsis: Implementation of the dot bracket annotations with Biostrings
Description:

The Structstrings package implements the widely used dot bracket annotation for storing base pairing information in structured RNA. Structstrings uses the infrastructure provided by the Biostrings package and derives the DotBracketString and related classes from the BString class. From these, base pair tables can be produced for in depth analysis. In addition, the loop indices of the base pairs can be retrieved as well. For better efficiency, information conversion is implemented in C, inspired to a large extend by the ViennaRNA package.

r-motifmatchr 1.30.0
Propagated dependencies: r-biostrings@2.76.0 r-bsgenome@1.76.0 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-matrix@1.7-3 r-rcpp@1.0.14 r-rcpparmadillo@14.4.3-1 r-rsamtools@2.24.0 r-s4vectors@0.46.0 r-summarizedexperiment@1.38.1 r-tfbstools@1.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/motifmatchr
Licenses: GPL 3
Synopsis: Fast motif matching in R
Description:

Quickly find motif matches for many motifs and many sequences. This package wraps C++ code from the MOODS motif calling library.

r-beadarraysnp 1.68.0
Propagated dependencies: r-biobase@2.68.0 r-quantsmooth@1.74.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/beadarraySNP
Licenses: GPL 2
Synopsis: Normalization and reporting of Illumina SNP bead arrays
Description:

This package is importing data from Illumina SNP experiments and it performs copy number calculations and reports.

r-samr 3.0
Propagated dependencies: r-gsa@1.03.3 r-impute@1.82.0 r-matrixstats@1.5.0 r-openxlsx@4.2.8 r-shiny@1.10.0 r-shinyfiles@0.9.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://statweb.stanford.edu/~tibs/SAM/
Licenses: LGPL 3+
Synopsis: Significance analysis of Microarrays
Description:

This is a package for significance analysis of Microarrays for differential expression analysis, RNAseq data and related problems.

r-fastseg 1.54.0
Propagated dependencies: r-biobase@2.68.0 r-biocgenerics@0.54.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioinf.jku.at/software/fastseg/index.html
Licenses: LGPL 2.0+
Synopsis: Fast segmentation algorithm for genetic sequencing data
Description:

Fastseg implements a very fast and efficient segmentation algorithm. It can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data.

r-clusterexperiment 2.28.1
Propagated dependencies: r-ape@5.8-1 r-biocgenerics@0.54.0 r-biocsingular@1.24.0 r-cluster@2.1.8.1 r-delayedarray@0.34.1 r-edger@4.6.2 r-hdf5array@1.36.0 r-kernlab@0.9-33 r-limma@3.64.1 r-locfdr@1.1-8 r-matrix@1.7-3 r-matrixstats@1.5.0 r-mbkmeans@1.24.0 r-nmf@0.28 r-phylobase@0.8.12 r-pracma@2.4.4 r-rcolorbrewer@1.1-3 r-rcpp@1.0.14 r-s4vectors@0.46.0 r-scales@1.4.0 r-singlecellexperiment@1.30.1 r-stringr@1.5.1 r-summarizedexperiment@1.38.1 r-zinbwave@1.30.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/clusterExperiment/
Licenses: Artistic License 2.0
Synopsis: Compare clusterings for single-cell sequencing
Description:

This package provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA expression data sets.

r-genomeinfodbdata 1.2.14
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GenomeInfoDbData
Licenses: Artistic License 2.0
Synopsis: Species and taxonomy ID look up tables for GenomeInfoDb
Description:

This package contains data for mapping between NCBI taxonomy ID and species. It is used by functions in the GenomeInfoDb package.

r-agimicrorna 2.58.0
Propagated dependencies: r-affy@1.86.0 r-affycoretools@1.80.0 r-biobase@2.68.0 r-limma@3.64.1 r-preprocesscore@1.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://git.bioconductor.org/packages/AgiMicroRna
Licenses: GPL 3
Synopsis: Processing and differential expression analysis of Agilent microRNA chips
Description:

AgiMicroRna provides useful functionality for the processing, quality assessment and differential expression analysis of Agilent microRNA array data. The package uses a limma-like structure to generate the processed data in order to make statistical inferences about differential expression using the linear model features implemented in limma. Standard Bioconductor objects are used so that other packages could be used as well.

r-org-dr-eg-db 3.21.0
Propagated dependencies: r-annotationdbi@1.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/org.Dr.eg.db/
Licenses: Artistic License 2.0
Synopsis: Annotation for Zebrafish
Description:

This package provides genome wide annotations for Zebrafish, primarily based on mapping using Entrez Gene identifiers.

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Total results: 45109