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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-airway 1.28.0
Propagated dependencies: r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/airway
Licenses: LGPL 2.0+
Synopsis: RangedSummarizedExperiment for RNA-Seq in airway smooth muscle cells
Description:

This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells. PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778.

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
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-rcy3 2.28.0
Propagated dependencies: r-base64enc@0.1-3 r-base64url@1.4 r-biocgenerics@0.54.0 r-fs@1.6.6 r-glue@1.8.0 r-gplots@3.2.0 r-graph@1.86.0 r-httr@1.4.7 r-irdisplay@1.1 r-irkernel@1.3.2 r-rcolorbrewer@1.1-3 r-rcurl@1.98-1.17 r-rjsonio@2.0.0 r-stringi@1.8.7 r-uuid@1.2-1 r-xml@3.99-0.18
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/cytoscape/RCy3
Licenses: Expat
Synopsis: Functions to access and control Cytoscape
Description:

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

r-icobra 1.36.0
Propagated dependencies: r-dplyr@1.1.4 r-dt@0.33 r-ggplot2@3.5.2 r-limma@3.64.1 r-markdown@2.0 r-reshape2@1.4.4 r-rlang@1.1.6 r-rocr@1.0-11 r-scales@1.4.0 r-shiny@1.10.0 r-shinybs@0.61.1 r-shinydashboard@0.7.3 r-upsetr@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/iCOBRA
Licenses: GPL 2+
Synopsis: Comparison and visualization of ranking and assignment methods
Description:

This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a Shiny application for interactive exploration of results.

r-genie3 1.30.0
Propagated dependencies: r-dplyr@1.1.4 r-reshape2@1.4.4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GENIE3
Licenses: GPL 2+
Synopsis: Gene network inference with ensemble of trees
Description:

This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.

r-msnid 1.42.0
Propagated dependencies: r-annotationdbi@1.70.0 r-annotationhub@3.16.0 r-biobase@2.68.0 r-biocgenerics@0.54.0 r-biocstyle@2.36.0 r-biostrings@2.76.0 r-data-table@1.17.4 r-doparallel@1.0.17 r-dplyr@1.1.4 r-foreach@1.5.2 r-ggplot2@3.5.2 r-iterators@1.0.14 r-msmstests@1.46.0 r-msnbase@2.34.1 r-mzid@1.46.0 r-mzr@2.42.0 r-protgenerics@1.40.0 r-purrr@1.0.4 r-r-cache@0.17.0 r-rcpp@1.0.14 r-reshape2@1.4.4 r-rlang@1.1.6 r-runit@0.4.33 r-stringr@1.5.1 r-tibble@3.2.1 r-xtable@1.8-4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MSnID
Licenses: Artistic License 2.0
Synopsis: Utilities for LC-MSn proteomics identifications
Description:

This package extracts tandem mass spectrometry (MS/MS) ID data from mzIdentML (leveraging the mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. It also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.

r-sictools 1.38.0
Dependencies: ncurses@6.2.20210619
Propagated dependencies: r-biostrings@2.76.0 r-doparallel@1.0.17 r-genomicranges@1.60.0 r-iranges@2.42.0 r-matrixstats@1.5.0 r-plyr@1.8.9 r-rsamtools@2.24.0 r-stringr@1.5.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/SICtools
Licenses: GPL 2+
Synopsis: Find SNV/Indel differences between two bam files with near relationship
Description:

This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison through each base position across the genome region of interest. The difference is inferred by Fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.

r-champdata 2.40.0
Propagated dependencies: r-biocgenerics@0.54.0 r-genomicranges@1.60.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ChAMPdata
Licenses: GPL 3
Synopsis: Data packages for ChAMP package
Description:

This package provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis.

r-fgsea 1.34.0
Propagated dependencies: r-bh@1.87.0-1 r-biocparallel@1.42.0 r-cowplot@1.1.3 r-data-table@1.17.4 r-fastmatch@1.1-6 r-ggplot2@3.5.2 r-matrix@1.7-3 r-rcpp@1.0.14 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ctlab/fgsea/
Licenses: Expat
Synopsis: Fast gene set enrichment analysis
Description:

The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm makes more permutations and gets more fine grained p-values, which allows using accurate standard approaches to multiple hypothesis correction.

r-rcistarget 1.28.1
Propagated dependencies: r-arrow@21.0.0 r-aucell@1.30.1 r-biocgenerics@0.54.0 r-data-table@1.17.4 r-dplyr@1.1.4 r-genomeinfodb@1.44.0 r-genomicranges@1.60.0 r-gseabase@1.70.0 r-r-utils@2.13.0 r-s4vectors@0.46.0 r-summarizedexperiment@1.38.1 r-tibble@3.2.1 r-zoo@1.8-14
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://aertslab.org/#scenic
Licenses: GPL 3
Synopsis: Identify transcription factor binding motifs enriched on a gene list
Description:

RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).

r-organism-dplyr 1.36.0
Propagated dependencies: r-annotationdbi@1.70.0 r-annotationfilter@1.32.0 r-biocfilecache@2.16.0 r-dbi@1.2.3 r-dbplyr@2.5.0 r-dplyr@1.1.4 r-genomeinfodb@1.44.0 r-genomicfeatures@1.60.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-rlang@1.1.6 r-rsqlite@2.3.11 r-s4vectors@0.46.0 r-tibble@3.2.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Organism.dplyr
Licenses: Artistic License 2.0
Synopsis: Dplyr-based access to Bioconductor annotation resources
Description:

This package provides an alternative interface to Bioconductor annotation resources, in particular the gene identifier mapping functionality of the org packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the TxDb packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).

r-ace 1.26.0
Propagated dependencies: r-biobase@2.68.0 r-genomicranges@1.60.0 r-ggplot2@3.5.2 r-qdnaseq@1.44.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/tgac-vumc/ACE
Licenses: GPL 2
Synopsis: Absolute copy number estimation from low-coverage whole genome sequencing
Description:

This package uses segmented copy number data to estimate tumor cell percentage and produce copy number plots displaying absolute copy numbers. For this it uses segmented data from the QDNAseq package, which in turn uses a number of dependencies to turn mapped reads into segmented data. ACE will run QDNAseq or use its output rds-file of segmented data. It will subsequently run through all samples in the object(s), for which it will create individual subdirectories. For each sample, it will calculate how well the segments fit (the relative error) to integer copy numbers for each percentage of tumor cells (cells with divergent segments).

r-bumphunter 1.50.0
Propagated dependencies: r-annotationdbi@1.70.0 r-biocgenerics@0.54.0 r-dorng@1.8.6.2 r-foreach@1.5.2 r-genomeinfodb@1.44.0 r-genomicfeatures@1.60.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-iterators@1.0.14 r-limma@3.64.1 r-locfit@1.5-9.12 r-matrixstats@1.5.0 r-s4vectors@0.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ririzarr/bumphunter
Licenses: Artistic License 2.0
Synopsis: Find bumps in genomic data
Description:

This package provides tools for finding bumps in genomic data in order to identify differentially methylated regions in epigenetic epidemiology studies.

r-biocor 1.32.0
Propagated dependencies: r-biocparallel@1.42.0 r-gseabase@1.70.0 r-matrix@1.7-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://llrs.github.io/BioCor/
Licenses: Expat
Synopsis: Functional similarities
Description:

This package provides tools to calculate functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships, and so on.

r-airpart 1.16.0
Propagated dependencies: r-apeglm@1.30.0 r-clue@0.3-66 r-complexheatmap@2.24.0 r-dplyr@1.1.4 r-dynamictreecut@1.63-1 r-emdbook@1.3.13 r-forestplot@3.1.6 r-ggplot2@3.5.2 r-lpsolve@5.6.23 r-matrixstats@1.5.0 r-mclust@6.1.1 r-pbapply@1.7-2 r-plyr@1.8.9 r-rcolorbrewer@1.1-3 r-rlang@1.1.6 r-s4vectors@0.46.0 r-scater@1.36.0 r-singlecellexperiment@1.30.1 r-smurf@1.1.7 r-summarizedexperiment@1.38.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/airpart
Licenses: GPL 2
Synopsis: Differential cell-type-specific allelic imbalance
Description:

The airpart package identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of a generalized fused lasso with binomial observations of allelic counts to partition cell types by their allelic imbalance. Alternatively, a nonparametric method for partitioning cell types is offered. The package includes a number of visualizations and quality control functions for examining single cell allelic imbalance datasets.

r-deconvr 1.14.0
Propagated dependencies: r-assertthat@0.2.1 r-biocgenerics@0.54.0 r-data-table@1.17.4 r-dplyr@1.1.4 r-e1071@1.7-16 r-foreach@1.5.2 r-genomicranges@1.60.0 r-iranges@2.42.0 r-magrittr@2.0.3 r-mass@7.3-65 r-matrixstats@1.5.0 r-methylkit@1.34.0 r-minfi@1.54.1 r-nnls@1.6 r-quadprog@1.5-8 r-rsq@2.7 r-s4vectors@0.46.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/BIMSBbioinfo/deconvR
Licenses: Artistic License 2.0
Synopsis: Simulation and deconvolution of omic profiles
Description:

This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types. The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally, we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.

r-epidish 2.24.0
Propagated dependencies: r-e1071@1.7-16 r-locfdr@1.1-8 r-mass@7.3-65 r-matrix@1.7-3 r-matrixstats@1.5.0 r-quadprog@1.5-8 r-stringr@1.5.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/sjczheng/EpiDISH
Licenses: GPL 2
Synopsis: Epigenetic dissection of intra-sample-heterogeneity
Description:

EpiDISH is a R package to infer the proportions of a priori known cell-types present in a sample representing a mixture of such cell-types. Right now, the package can be used on DNAm data of whole blood, generic epithelial tissue and breast tissue. Besides, the package provides a function that allows the identification of differentially methylated cell-types and their directionality of change in Epigenome-Wide Association Studies.

r-copynumber 1.38.0
Propagated dependencies: r-s4vectors@0.46.0 r-iranges@2.42.0 r-genomicranges@1.60.0 r-biocgenerics@0.54.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/copynumber
Licenses: Artistic License 2.0
Synopsis: Segmentation of single- and multi-track copy number data
Description:

This package segments single- and multi-track copy number data by a penalized least squares regression method.

r-structuralvariantannotation 1.24.0
Propagated dependencies: r-assertthat@0.2.1 r-biocgenerics@0.54.0 r-biostrings@2.76.0 r-dplyr@1.1.4 r-genomeinfodb@1.44.0 r-genomicfeatures@1.60.0 r-genomicranges@1.60.0 r-iranges@2.42.0 r-pwalign@1.4.0 r-rlang@1.1.6 r-rtracklayer@1.68.0 r-s4vectors@0.46.0 r-stringr@1.5.1 r-summarizedexperiment@1.38.1 r-variantannotation@1.54.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/StructuralVariantAnnotation/
Licenses: GPL 3
Synopsis: R package designed to simplify structural variant analysis
Description:

This package contains useful helper functions for dealing with structural variants in VCF format. The packages contains functions for parsing VCFs from a number of popular callers as well as functions for dealing with breakpoints involving two separate genomic loci encoded as GRanges objects.

r-triform 1.29.0
Propagated dependencies: r-biocgenerics@0.54.0 r-iranges@2.42.0 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/triform/
Licenses: GPL 2
Synopsis: Find enriched regions in transcription factor ChIP-sequencing data
Description:

The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.

r-illumina450probevariants-db 1.44.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Illumina450ProbeVariants.db
Licenses: GPL 3
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-aldex2 1.40.0
Propagated dependencies: r-biocparallel@1.42.0 r-directlabels@2025.5.20 r-genomicranges@1.60.0 r-iranges@2.42.0 r-lattice@0.22-7 r-latticeextra@0.6-30 r-multtest@2.64.0 r-rfast@2.1.5.1 r-s4vectors@0.46.0 r-summarizedexperiment@1.38.1 r-zcompositions@1.5.0-4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ggloor/ALDEx_bioc
Licenses: AGPL 3+ GPL 2+ GPL 3
Synopsis: Analysis of differential abundance taking sample variation into account
Description:

This package provides a differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch's t-test, a Kruskal-Wallis test, a generalized linear model, or a correlation test. All tests report p-values and Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs.

r-a4classif 1.56.0
Propagated dependencies: r-a4core@1.56.0 r-a4preproc@1.56.0 r-biobase@2.68.0 r-glmnet@4.1-8 r-pamr@1.57 r-rocr@1.0-11 r-varselrf@0.7-8
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/a4Classif/
Licenses: GPL 3
Synopsis: Automated Affymetrix array analysis classification package
Description:

This is the classification package for the automated analysis of Affymetrix arrays.

r-biomartr 1.0.7
Propagated dependencies: r-biomart@2.64.0 r-biostrings@2.76.0 r-curl@6.2.3 r-data-table@1.17.4 r-downloader@0.4.1 r-dplyr@1.1.4 r-fs@1.6.6 r-httr@1.4.7 r-jsonlite@2.0.0 r-philentropy@0.9.0 r-purrr@1.0.4 r-r-utils@2.13.0 r-rcurl@1.98-1.17 r-readr@2.1.5 r-stringr@1.5.1 r-tibble@3.2.1 r-withr@3.0.2 r-xml@3.99-0.18
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://docs.ropensci.org/biomartr/
Licenses: GPL 2
Synopsis: Genomic data retrieval
Description:

Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, RNA, coding sequence (CDS), GFF, and metagenome retrieval from NCBI RefSeq, NCBI Genbank, ENSEMBL, and UniProt databases. Furthermore, an interface to the BioMart database allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as NCBI RefSeq, NCBI nr, NCBI nt, NCBI Genbank, etc with only one command.

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Total results: 45109