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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-aggregatebiovar 1.18.0
Propagated dependencies: r-matrix@1.7-3 r-rlang@1.1.6 r-s4vectors@0.46.0 r-singlecellexperiment@1.30.1 r-summarizedexperiment@1.38.1 r-tibble@3.2.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/jasonratcliff/aggregateBioVar
Licenses: GPL 3
Synopsis: Differential gene expression analysis for multi-subject scRNA-seq
Description:

This package aggregateBioVar contains tools to summarize single cell gene expression profiles at the level of subject for single cell RNA-seq data collected from more than one subject (e.g. biological sample or technical replicates). A SingleCellExperiment object is taken as input and converted to a list of SummarizedExperiment objects, where each list element corresponds to an assigned cell type. The SummarizedExperiment objects contain aggregate gene-by-subject count matrices and inter-subject column metadata for individual subjects that can be processed using downstream bulk RNA-seq tools.

r-aseb 1.52.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ASEB
Licenses: GPL 3+
Synopsis: Predict acetylated lysine sites
Description:

ASEB is an R package to predict lysine sites that can be acetylated by a specific KAT (K-acetyl-transferases) family. Lysine acetylation is a well-studied posttranslational modification on kinds of proteins. About four thousand lysine acetylation sites and over 20 lysine KATs have been identified. However, which KAT is responsible for a given protein or lysine site acetylation is mostly unknown. In this package, we use a GSEA-like (Gene Set Enrichment Analysis) method to make predictions. GSEA method was developed and successfully used to detect coordinated expression changes and find the putative functions of the long non-coding RNAs.

r-somaticsignatures 2.44.0
Propagated dependencies: r-biobase@2.68.0 r-biostrings@2.76.0 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-ggbio@1.56.0 r-ggplot2@3.5.2 r-iranges@2.42.0 r-nmf@0.28 r-pcamethods@2.0.0 r-proxy@0.4-27 r-reshape2@1.4.4 r-s4vectors@0.46.0 r-variantannotation@1.54.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/juliangehring/SomaticSignatures
Licenses: Expat
Synopsis: Somatic signatures
Description:

This package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.

r-homo-sapiens 1.3.1
Propagated dependencies: r-annotationdbi@1.70.0 r-genomicfeatures@1.60.0 r-go-db@3.21.0 r-org-hs-eg-db@3.21.0 r-organismdbi@1.50.0 r-txdb-hsapiens-ucsc-hg19-knowngene@3.2.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Homo.sapiens/
Licenses: Artistic License 2.0
Synopsis: Annotation package for the Homo.sapiens object
Description:

This package contains the Homo.sapiens object to access data from several related annotation packages.

r-ggtreeextra 1.18.0
Propagated dependencies: r-cli@3.6.5 r-ggnewscale@0.5.1 r-ggplot2@3.5.2 r-ggtree@3.16.0 r-magrittr@2.0.3 r-rlang@1.1.6 r-tidytree@0.4.6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/YuLab-SMU/ggtreeExtra/
Licenses: GPL 3+
Synopsis: Add geometric layers On circular or other layout tree of ggtree
Description:

ggtreeExtra extends the method for mapping and visualizing associated data on phylogenetic tree using ggtree. These associated data can be presented on the external panels to circular layout, fan layout, or other rectangular layout tree built by ggtree with the grammar of ggplot2.

r-affyrnadegradation 1.54.0
Propagated dependencies: r-affy@1.86.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AffyRNADegradation
Licenses: GPL 2+
Synopsis: Analyze and correct probe positional bias in data due to RNA degradation
Description:

The AffyRNADegradation package helps with the assessment and correction of RNA degradation effects in Affymetrix 3 expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

r-hyperdraw 1.60.0
Dependencies: graphviz@7.0.1
Propagated dependencies: r-graph@1.86.0 r-hypergraph@1.80.0 r-rgraphviz@2.52.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/hyperdraw
Licenses: GPL 2+
Synopsis: Visualizing hypergraphs
Description:

This package provides functions for visualizing hypergraphs.

r-ruvseq 1.42.0
Propagated dependencies: r-biobase@2.68.0 r-edaseq@2.42.0 r-edger@4.6.2 r-mass@7.3-65
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/drisso/RUVSeq
Licenses: Artistic License 2.0
Synopsis: Remove unwanted variation from RNA-Seq data
Description:

This package implements methods to remove unwanted variation (RUV) of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.

r-decipher 3.4.0
Propagated dependencies: r-biostrings@2.76.0 r-dbi@1.2.3 r-iranges@2.42.0 r-s4vectors@0.46.0 r-xvector@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/DECIPHER/
Licenses: GPL 3
Synopsis: Tools for deciphering and managing biological sequences
Description:

This package provides a toolset for deciphering and managing biological sequences.

r-anvilgcp 1.2.0
Propagated dependencies: r-anvilbase@1.2.0 r-biocbaseutils@1.10.0 r-dplyr@1.1.4 r-httr@1.4.7 r-jsonlite@2.0.0 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/Bioconductor/AnVILGCP
Licenses: Artistic License 2.0
Synopsis: GCP R client for the AnVIL
Description:

The package provides a set of functions to interact with the Google Cloud Platform (GCP) services on the AnVIL platform. The package is designed to work with the AnVIL package. User-level interaction with this package should be minimal.

r-biobtreer 1.20.0
Propagated dependencies: r-httpuv@1.6.16 r-httr@1.4.7 r-jsonlite@2.0.0 r-stringi@1.8.7
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/tamerh/biobtreeR
Licenses: Expat
Synopsis: Use biobtree tool from R
Description:

The biobtreeR package provides an interface to biobtree, a tool which covers large sets of bioinformatics datasets and allows search and chain mappings functionalities.

r-dyndoc 1.86.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/DynDoc
Licenses: Artistic License 2.0
Synopsis: Dynamic document tools
Description:

This package provides a set of functions to create and interact with dynamic documents and vignettes.

r-annotatr 1.34.0
Propagated dependencies: r-annotationdbi@1.70.0 r-annotationhub@3.16.0 r-dplyr@1.1.4 r-genomeinfodb@1.44.0 r-genomicfeatures@1.60.0 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-iranges@2.42.0 r-readr@2.1.5 r-regioner@1.39.0 r-reshape2@1.4.4 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/annotatr/
Licenses: GPL 3
Synopsis: Annotation of genomic regions to genomic annotations
Description:

Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.

r-msdata 0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/msdata
Licenses: GPL 2+
Synopsis: Various Mass Spectrometry raw data example files
Description:

This package provides Ion Trap positive ionization mode data in mzML file format. It includes a subset from 500-850 m/z and 1190-1310 seconds, including MS2 and MS3, intensity threshold 100.000; extracts from FTICR Apex III, m/z 400-450; a subset of UPLC - Bruker micrOTOFq data, both mzML and mz5; LC-MSMS and MRM files from proteomics experiments; and PSI mzIdentML example files for various search engines.

r-raggedexperiment 1.32.2
Propagated dependencies: r-biocbaseutils@1.10.0 r-biocgenerics@0.54.0 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-matrix@1.7-3 r-matrixgenerics@1.20.0 r-s4vectors@0.46.0 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/RaggedExperiment
Licenses: Artistic License 2.0
Synopsis: Representation of sparse experiments and assays across samples
Description:

This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns. The RaggedExperiment class derives from a GRangesList representation and provides a semblance of a rectangular dataset.

r-scannotatr 1.14.0
Propagated dependencies: r-annotationhub@3.16.0 r-ape@5.8-1 r-caret@7.0-1 r-data-tree@1.1.0 r-dplyr@1.1.4 r-e1071@1.7-16 r-ggplot2@3.5.2 r-kernlab@0.9-33 r-proc@1.18.5 r-rocr@1.0-11 r-seurat@5.3.0 r-singlecellexperiment@1.30.1 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/grisslab/scAnnotatR
Licenses: Expat
Synopsis: Pretrained models for prediction on single cell RNA-sequencing data
Description:

This package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables to quickly get a first annotation of the cell types present in the dataset without requiring prior knowledge. The package also lets you train using own models to predict new cell types based on specific research needs.

r-r3cseq 1.54.0
Propagated dependencies: r-biostrings@2.76.0 r-data-table@1.17.4 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-qvalue@2.40.0 r-rcolorbrewer@1.1-3 r-rsamtools@2.24.0 r-rtracklayer@1.68.0 r-sqldf@0.4-11 r-vgam@1.1-13
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://r3cseq.genereg.net/Site/index.html
Licenses: GPL 3
Synopsis: Analysis of Chromosome conformation capture and Next-generation sequencing
Description:

This package is used for the analysis of long-range chromatin interactions from 3C-seq assay.

r-gtrellis 1.40.0
Propagated dependencies: r-circlize@0.4.16 r-genomicranges@1.60.0 r-getoptlong@1.0.5 r-iranges@2.42.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/jokergoo/gtrellis
Licenses: Expat
Synopsis: Genome level Trellis layout
Description:

Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.

r-riboprofiling 1.38.0
Propagated dependencies: r-biocgenerics@0.54.0 r-biostrings@2.76.0 r-data-table@1.17.4 r-genomeinfodb@1.44.0 r-genomicalignments@1.44.0 r-genomicfeatures@1.60.0 r-genomicranges@1.60.0 r-ggbio@1.56.0 r-ggplot2@3.5.2 r-iranges@2.42.0 r-plyr@1.8.9 r-reshape2@1.4.4 r-rsamtools@2.24.0 r-rtracklayer@1.68.0 r-s4vectors@0.46.0 r-sqldf@0.4-11
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/RiboProfiling/
Licenses: GPL 3
Synopsis: Ribosome profiling data analysis
Description:

Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.

r-asafe 1.34.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ASAFE
Licenses: Artistic License 2.0
Synopsis: Ancestry Specific Allele Frequency Estimation
Description:

The ASAFE package contains a collection of functions that can be used to carry out an EM (Expectation–maximization) algorithm to estimate ancestry-specific allele frequencies for a bi-allelic genetic marker, e.g. an SNP (single nucleotide polymorphism) from genotypes and ancestry pairs.

r-rhdf5lib 1.30.0
Propagated dependencies: hdf5@1.10.9 zlib@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Rhdf5lib
Licenses: Artistic License 2.0
Synopsis: HDF5 library as an R package
Description:

This package provides C and C++ HDF5 libraries for use in R packages.

r-fhtest 1.5.1
Propagated dependencies: r-interval@1.1-1.0 r-kmsurv@0.1-6 r-mass@7.3-65 r-perm@1.0-0.4 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/web/packages/FHtest/
Licenses: GPL 2+
Synopsis: Tests for survival data based on the Fleming-Harrington class
Description:

This package provides functions to compare two or more survival curves with:

  • The Fleming-Harrington test for right-censored data based on permutations and on counting processes.

  • An extension of the Fleming-Harrington test for interval-censored data based on a permutation distribution and on a score vector distribution.

r-hgu95av2-db 3.13.0
Propagated dependencies: r-annotationdbi@1.70.0 r-org-hs-eg-db@3.21.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/hgu95av2.db
Licenses: Artistic License 2.0
Synopsis: Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2)
Description:

This package provides Affymetrix HG_U95Av2 Array annotation data (chip hgu95av2) assembled using data from public repositories.

r-arraymvout 1.66.0
Propagated dependencies: r-affy@1.86.0 r-affycontam@1.66.0 r-biobase@2.68.0 r-lumi@2.60.0 r-mdqc@1.70.0 r-parody@1.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/arrayMvout
Licenses: Artistic License 2.0
Synopsis: Multivariate outlier detection for expression array QA
Description:

This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate.

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Total results: 45109