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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-riboseqr 1.44.0
Propagated dependencies: r-abind@1.4-8 r-bayseq@2.44.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-seqlogo@1.76.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/riboSeqR/
Licenses: GPL 3
Build system: r
Synopsis: Analysis of sequencing data from ribosome profiling experiments
Description:

This package provides plotting functions, frameshift detection and parsing of genetic sequencing data from ribosome profiling experiments.

r-hgu95av2cdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/hgu95av2cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: hgu95av2cdf
Description:

This package provides a package containing an environment representing the HG_U95Av2.CDF file.

r-flowmeans 1.70.0
Propagated dependencies: r-biobase@2.70.0 r-feature@1.2.15 r-flowcore@2.22.0 r-rrcov@1.7-7
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/flowMeans
Licenses: Artistic License 2.0
Build system: r
Synopsis: Non-parametric flow cytometry data gating
Description:

This package provides tools to identify cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection.

r-chicago 1.38.0
Propagated dependencies: r-data-table@1.17.8 r-delaporte@8.4.2 r-hmisc@5.2-4 r-mass@7.3-65 r-matrixstats@1.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Chicago
Licenses: Artistic License 2.0
Build system: r
Synopsis: Capture Hi-C analysis of genomic organization
Description:

This package provides a pipeline for analysing Capture Hi-C data.

r-convert 1.86.0
Propagated dependencies: r-biobase@2.70.0 r-limma@3.66.0 r-marray@1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://bioinf.wehi.edu.au/limma/convert.html
Licenses: LGPL 2.0+
Build system: r
Synopsis: Convert microarray data objects
Description:

This package defines coerce methods for microarray data objects.

r-roc 1.86.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/ROC/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Utilities for ROC curves
Description:

This package provides utilities for Receiver Operating Characteristic (ROC) curves, with a focus on micro arrays.

r-maftools 2.26.0
Propagated dependencies: r-data-table@1.17.8 r-dnacopy@1.84.0 r-pheatmap@1.0.13 r-rcolorbrewer@1.1-3 r-rhtslib@3.6.0 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/PoisonAlien/maftools
Licenses: Expat
Build system: r
Synopsis: Summarize, analyze and visualize MAF files
Description:

Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.

r-hgu95av2 2.2.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/hgu95av2
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Human Genome U95 Set annotation data (hgu95av2)
Description:

This package provides Affymetrix Human Genome U95 Set annotation data (hgu95av2) assembled using data from public data repositories.

r-webbioc 1.82.0
Dependencies: netpbm@10.78.3 perl@5.36.0
Propagated dependencies: r-affy@1.88.0 r-annaffy@1.82.0 r-biobase@2.70.0 r-biocmanager@1.30.27 r-gcrma@2.82.0 r-multtest@2.66.0 r-qvalue@2.42.0 r-vsn@3.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/
Licenses: GPL 2+
Build system: r
Synopsis: Bioconductor web interface
Description:

This package provides an integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. Currently only Affymetrix oligonucleotide analysis is supported.

r-xcms 4.8.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-data-table@1.17.8 r-iranges@2.44.0 r-lattice@0.22-7 r-massspecwavelet@1.76.0 r-metabocoreutils@1.18.1 r-mscoreutils@1.21.0 r-msexperiment@1.12.0 r-msfeatures@1.18.0 r-msnbase@2.36.0 r-mzr@2.44.0 r-progress@1.2.3 r-protgenerics@1.42.0 r-rcolorbrewer@1.1-3 r-s4vectors@0.48.0 r-spectra@1.20.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/xcms/
Licenses: GPL 2+
Build system: r
Synopsis: LC/MS and GC/MS mass spectrometry data analysis
Description:

This package provides a framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. It imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses data for high-throughput, untargeted analyte profiling.

r-gosemsim 2.36.0
Propagated dependencies: r-annotationdbi@1.72.0 r-dbi@1.2.3 r-digest@0.6.39 r-go-db@3.22.0 r-r-utils@2.13.0 r-rcpp@1.1.0 r-rlang@1.1.6 r-yulab-utils@0.2.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://guangchuangyu.github.io/software/GOSemSim
Licenses: Artistic License 2.0
Build system: r
Synopsis: GO-terms semantic similarity measures
Description:

The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters.

r-tximportdata 1.38.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/tximportData
Licenses: GPL 2+
Build system: r
Synopsis: Data for the tximport package
Description:

This package provides the output of running various transcript abundance quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The quantifiers were Cufflinks, RSEM, kallisto, Salmon and Sailfish. Alevin example output is also included.

r-txdb-hsapiens-ucsc-hg19-knowngene 3.22.1
Propagated dependencies: r-annotationdbi@1.72.0 r-genomicfeatures@1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for human genome in TxDb format
Description:

This package provides an annotation database of Homo sapiens genome data. It is derived from the UCSC hg19 genome and based on the "knownGene" track. The database is exposed as a TxDb object.

r-breakpointrdata 1.28.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/daewoooo/breakpointRdata
Licenses: Expat
Build system: r
Synopsis: Strand-seq data for demonstration purposes
Description:

This package is a collection of Strand-seq data. The main purpose is to demonstrate functionalities of the breakpointR package.

r-bsgenome-dmelanogaster-ucsc-dm3-masked 1.3.99
Propagated dependencies: r-bsgenome@1.78.0 r-bsgenome-dmelanogaster-ucsc-dm3@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full masked genome sequences for Fly
Description:

This package provides full masked genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm3, 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), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

r-hyperdraw 1.62.0
Dependencies: graphviz@7.0.1
Propagated dependencies: r-graph@1.88.0 r-hypergraph@1.82.0 r-rgraphviz@2.54.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/hyperdraw
Licenses: GPL 2+
Build system: r
Synopsis: Visualizing hypergraphs
Description:

This package provides functions for visualizing hypergraphs.

r-genomicinteractions 1.44.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-gridextra@2.3 r-gviz@1.54.0 r-igraph@2.2.1 r-interactionset@1.38.0 r-iranges@2.44.0 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/
Licenses: GPL 3
Build system: r
Synopsis: R package for handling genomic interaction data
Description:

This R package provides tools for handling genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots and statistics.

r-go-db 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GO.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation maps describing the entire Gene Ontology
Description:

The purpose of this GO.db annotation package is to provide detailed information about the latest version of the Gene Ontologies.

r-annotationforge 1.52.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-dbi@1.2.3 r-rcurl@1.98-1.17 r-rsqlite@2.4.4 r-s4vectors@0.48.0 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AnnotationForge
Licenses: Artistic License 2.0
Build system: r
Synopsis: Code for building annotation database packages
Description:

This package provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.

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+
Build system: r
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-abaenrichment 1.24.0
Propagated dependencies: r-abadata@1.12.0 r-data-table@1.17.8 r-gofuncr@1.30.0 r-gplots@3.2.0 r-gtools@3.9.5 r-rcpp@1.1.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ABAEnrichment/
Licenses: GPL 2+
Build system: r
Synopsis: Gene expression enrichment in human brain regions
Description:

The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function aba_enrich integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project.

r-infercnv 1.26.0
Dependencies: python@3.11.14
Propagated dependencies: r-ape@5.8-1 r-argparse@2.3.1 r-biocgenerics@0.56.0 r-catools@1.18.3 r-coda@0.19-4.1 r-coin@1.4-3 r-digest@0.6.39 r-doparallel@1.0.17 r-dplyr@1.1.4 r-edger@4.8.0 r-fastcluster@1.3.0 r-fitdistrplus@1.2-4 r-foreach@1.5.2 r-futile-logger@1.4.3 r-future@1.68.0 r-ggplot2@4.0.1 r-gplots@3.2.0 r-gridextra@2.3 r-hiddenmarkov@1.8-14 r-igraph@2.2.1 r-matrix@1.7-4 r-paralleldist@0.2.7 r-phyclust@0.1-34 r-rann@2.6.2 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-rjags@4-17 r-seurat@5.3.1 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/broadinstitute/inferCNV/wiki
Licenses: Modified BSD
Build system: r
Synopsis: Infer copy number variation from single-cell RNA-Seq data
Description:

InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence for somatic large-scale chromosomal copy number alterations, such as gains or deletions of entire chromosomes or large segments of chromosomes. This is done by exploring expression intensity of genes across positions of a tumor genome in comparison to a set of reference "normal" cells. A heatmap is generated illustrating the relative expression intensities across each chromosome, and it often becomes readily apparent as to which regions of the tumor genome are over-abundant or less-abundant as compared to that of normal cells.

r-seqpattern 1.42.0
Propagated dependencies: r-biostrings@2.78.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-kernsmooth@2.23-26 r-plotrix@3.8-13
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/seqPattern
Licenses: GPL 3+
Build system: r
Synopsis: Visualising oligonucleotide patterns and motif occurrences
Description:

This package provides tools to visualize oligonucleotide patterns and sequence motif occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.

r-m3c 1.32.0
Propagated dependencies: r-cluster@2.1.8.1 r-corpcor@1.6.10 r-doparallel@1.0.17 r-dosnow@1.0.20 r-foreach@1.5.2 r-ggplot2@4.0.1 r-matrix@1.7-4 r-matrixcalc@1.0-6 r-rtsne@0.17 r-umap@0.2.10.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/M3C
Licenses: AGPL 3+
Build system: r
Synopsis: Monte Carlo reference-based consensus clustering
Description:

M3C is a consensus clustering algorithm that uses a Monte Carlo simulation to eliminate overestimation of K and can reject the null hypothesis K=1.

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