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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-mosdef 1.6.0
Propagated dependencies: r-annotationdbi@1.72.0 r-clusterprofiler@4.18.2 r-deseq2@1.50.2 r-dt@0.34.0 r-ggforce@0.5.0 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-go-db@3.22.0 r-goseq@1.62.0 r-htmltools@0.5.8.1 r-rcolorbrewer@1.1-3 r-rlang@1.1.6 r-s4vectors@0.48.0 r-scales@1.4.0 r-summarizedexperiment@1.40.0 r-topgo@2.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/imbeimainz/mosdef
Licenses: Expat
Build system: r
Synopsis: Frequently used and useful differential expression functions
Description:

This package provides functionality to run a number of tasks in the differential expression analysis workflow. This encompasses the most widely used steps, from running various enrichment analysis tools with a unified interface to creating plots and beautifying table components linking to external websites and databases. This streamlines the generation of comprehensive analysis reports.

r-mscoreutils 1.21.0
Propagated dependencies: r-clue@0.3-66 r-mass@7.3-65 r-rcpp@1.1.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/RforMassSpectrometry/MsCoreUtils
Licenses: Artistic License 2.0
Build system: r
Synopsis: Core utils for mass spectrometry data
Description:

This package defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning), quantitative aggregation functions (median polish, robust summarisation, etc.), missing data imputation, data normalisation (quantiles, vsn, etc.) as well as misc helper functions, that are used across high-level data structure within the R for Mass Spectrometry packages.

r-absseq 1.64.0
Propagated dependencies: r-limma@3.66.0 r-locfit@1.5-9.12
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ABSSeq
Licenses: GPL 3+
Build system: r
Synopsis: RNA-Seq analysis based on modelling absolute expression differences
Description:

This package implements a new RNA-Seq analysis method and integrates two modules: a basic model for pairwise comparison and a linear model for complex design. RNA-Seq quantifies gene expression with reads count, which usually consists of conditions (or treatments) and several replicates for each condition. This software infers differential expression directly by the counts difference between conditions. It assumes that the sum counts difference between conditions follow a negative binomial distribution. In addition, ABSSeq moderates the fold-changes by two steps: the expression level and gene-specific dispersion, that might facilitate the gene ranking by fold-change and visualization.

r-parody 1.68.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/parody
Licenses: Artistic License 2.0
Build system: r
Synopsis: Parametric and resistant outlier detection
Description:

The parody package provides routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics.

r-biocversion 3.22.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BiocVersion/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Set the appropriate version of Bioconductor packages
Description:

This package provides repository information for the appropriate version of Bioconductor.

r-mbecs 1.14.0
Propagated dependencies: r-cluster@2.1.8.1 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-gridextra@2.3 r-limma@3.66.0 r-lme4@1.1-37 r-lmertest@3.1-3 r-magrittr@2.0.4 r-matrix@1.7-4 r-pheatmap@1.0.13 r-phyloseq@1.54.0 r-rmarkdown@2.30 r-ruv@0.9.7.1 r-sva@3.58.0 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://github.com/rmolbrich/MBECS
Licenses: Artistic License 2.0
Build system: r
Synopsis: Evaluation and correction of batch effects in microbiome data-sets
Description:

The MBECS provides a set of functions to evaluate and mitigate unwated noise due to processing in batches. To that end it incorporates a host of batch correcting algorithms (BECA) from various packages. In addition it offers a correction and reporting pipeline that provides a preliminary look at the characteristics of a data-set before and after correcting for batch effects.

r-transcriptr 1.37.0
Propagated dependencies: r-biocgenerics@0.56.0 r-caret@7.0-1 r-chipseq@1.60.0 r-e1071@1.7-16 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-proc@1.19.0.1 r-reshape2@1.4.5 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/transcriptR
Licenses: GPL 3
Build system: r
Synopsis: Primary transcripts detection and quantification
Description:

The differences in the RNA types being sequenced have an impact on the resulting sequencing profiles. mRNA-seq data is enriched with reads derived from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial broader coverage of both exonic and intronic regions. The presence of intronic reads in GRO-seq type of data makes it possible to use it to computationally identify and quantify all de novo continuous regions of transcription distributed across the genome. This type of data, however, is more challenging to interpret and less common practice compared to mRNA-seq. One of the challenges for primary transcript detection concerns the simultaneous transcription of closely spaced genes, which needs to be properly divided into individually transcribed units. The R package transcriptR combines RNA-seq data with ChIP-seq data of histone modifications that mark active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to overcome this challenge. The advantage of this approach over the use of, for example, gene annotations is that this approach is data driven and therefore able to deal also with novel and case specific events.

r-modstrings 1.26.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-crayon@1.5.3 r-genomicranges@1.62.0 r-iranges@2.44.0 r-s4vectors@0.48.0 r-stringi@1.8.7 r-stringr@1.6.0 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Modstrings
Licenses: Artistic License 2.0
Build system: r
Synopsis: Working with modified nucleotide sequences
Description:

Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionality for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.

r-multidataset 1.38.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-iranges@2.44.0 r-limma@3.66.0 r-qqman@0.1.9 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MultiDataSet/
Licenses: Expat
Build system: r
Synopsis: Implementation of MultiDataSet and ResultSet
Description:

This package provides an implementation of the BRGE's (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages.

r-msmseda 1.48.0
Propagated dependencies: r-gplots@3.2.0 r-mass@7.3-65 r-msnbase@2.36.0 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
Build system: r
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-apcomplex 2.76.0
Propagated dependencies: r-graph@1.88.0 r-org-sc-sgd-db@3.22.0 r-rbgl@1.86.0 r-rgraphviz@2.54.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/apComplex
Licenses: LGPL 2.0+
Build system: r
Synopsis: Estimate protein complex membership using AP-MS protein data
Description:

This package provides functions to estimate a bipartite graph of protein complex membership using AP-MS data.

r-biomformat 1.38.0
Propagated dependencies: r-jsonlite@2.0.0 r-matrix@1.7-4 r-plyr@1.8.9 r-rhdf5@2.54.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/joey711/biomformat/
Licenses: GPL 2
Build system: r
Synopsis: Interface package for the BIOM file format
Description:

This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the Python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.

r-gofuncr 1.30.0
Propagated dependencies: r-annotationdbi@1.72.0 r-genomicranges@1.62.0 r-gtools@3.9.5 r-iranges@2.44.0 r-mapplots@1.5.3 r-rcpp@1.1.0 r-vioplot@0.5.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GOfuncR/
Licenses: GPL 2+
Build system: r
Synopsis: Gene ontology enrichment using FUNC
Description:

GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages (Homo.sapiens by default); the GO-graph is included in the package and updated regularly. GOfuncR provides the standard candidate vs background enrichment analysis using the hypergeometric test, as well as three additional tests:

  1. the Wilcoxon rank-sum test that is used when genes are ranked,

  2. a binomial test that is used when genes are associated with two counts, and

  3. a Chi-square or Fisher's exact test that is used in cases when genes are associated with four counts.

To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.

r-sanssouci 0-1.5fe20a9
Propagated dependencies: r-generics@0.1.4 r-matrix@1.7-4 r-matrixstats@1.5.0 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://pneuvial.github.io/sanssouci
Licenses: GPL 3
Build system: r
Synopsis: Post Hoc multiple testing inference
Description:

The goal of sansSouci is to perform post hoc inference: in a multiple testing context, sansSouci provides statistical guarantees on possibly user-defined and/or data-driven sets of hypotheses.

r-ncdfflow 2.56.0
Propagated dependencies: r-bh@1.87.0-1 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-cpp11@0.5.2 r-flowcore@2.22.0 r-rhdf5lib@1.32.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ncdfFlow/
Licenses: Artistic License 2.0
Build system: r
Synopsis: HDF5 based storage for flow cytometry data
Description:

This package provides HDF5 storage based methods and functions for manipulation of flow cytometry data.

r-circrnaprofiler 1.24.0
Propagated dependencies: r-annotationhub@4.0.0 r-biostrings@2.78.0 r-bsgenome@1.78.0 r-bsgenome-hsapiens-ucsc-hg19@1.4.3 r-deseq2@1.50.2 r-dplyr@1.1.4 r-edger@4.8.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-gwascat@2.42.0 r-iranges@2.44.0 r-magrittr@2.0.4 r-r-utils@2.13.0 r-readr@2.1.6 r-reshape2@1.4.5 r-rlang@1.1.6 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinr@4.2-36 r-stringi@1.8.7 r-stringr@1.6.0 r-universalmotif@1.28.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/Aufiero/circRNAprofiler
Licenses: GPL 3
Build system: r
Synopsis: Computational framework for the downstream analysis of circular RNA's
Description:

r-circrnaprofiler is a computational framework for a comprehensive in silico analysis of circular RNA (circRNAs). This computational framework allows combining and analyzing circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis.

r-interval 1.1-1.0
Propagated dependencies: r-icens@1.82.0 r-mlecens@0.1-7.1 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/interval/
Licenses: GPL 2+
Build system: r
Synopsis: Weighted Logrank tests and NPMLE for interval censored data
Description:

This package provides functions to fit nonparametric survival curves, plot them, and perform logrank or Wilcoxon type tests.

r-opencyto 2.22.0
Propagated dependencies: r-bh@1.87.0-1 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-cpp11@0.5.2 r-data-table@1.17.8 r-flowclust@3.48.0 r-flowcore@2.22.0 r-flowviz@1.74.0 r-flowworkspace@4.22.0 r-graph@1.88.0 r-ncdfflow@2.56.0 r-rbgl@1.86.0 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/openCyto
Licenses: Artistic License 2.0
Build system: r
Synopsis: Hierarchical gating pipeline for flow cytometry data
Description:

This package is designed to facilitate the automated gating methods in a sequential way to mimic the manual gating strategy.

r-complexheatmap 2.26.0
Propagated dependencies: r-circlize@0.4.16 r-clue@0.3-66 r-codetools@0.2-20 r-colorspace@2.1-2 r-digest@0.6.39 r-doparallel@1.0.17 r-foreach@1.5.2 r-getoptlong@1.0.5 r-globaloptions@0.1.2 r-iranges@2.44.0 r-matrixstats@1.5.0 r-png@0.1-8 r-rcolorbrewer@1.1-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/jokergoo/ComplexHeatmap
Licenses: GPL 2+
Build system: r
Synopsis: Making Complex Heatmaps
Description:

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential structures. This package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.

r-beadarraysnp 1.68.0
Propagated dependencies: r-biobase@2.70.0 r-quantsmooth@1.76.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/beadarraySNP
Licenses: GPL 2
Build system: r
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-scmap 1.32.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-dplyr@1.1.4 r-e1071@1.7-16 r-ggplot2@4.0.1 r-googlevis@0.7.3 r-matrixstats@1.5.0 r-proxy@0.4-27 r-randomforest@4.7-1.2 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1 r-reshape2@1.4.5 r-s4vectors@0.48.0 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/hemberg-lab/scmap
Licenses: GPL 3
Build system: r
Synopsis: Tool for unsupervised projection of single cell RNA-seq data
Description:

Single-cell RNA-seq (scRNA-seq) is widely used to investigate the composition of complex tissues since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome. However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. scmap is a method for projecting cells from a scRNA-seq experiment onto the cell-types or individual cells identified in a different experiment.

r-bayesknockdown 1.36.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BayesKnockdown
Licenses: GPL 3
Build system: r
Synopsis: Posterior probabilities for edges from knockdown data
Description:

This package provides a simple, fast Bayesian method for computing posterior probabilities for relationships between a single predictor variable and multiple potential outcome variables, incorporating prior probabilities of relationships. In the context of knockdown experiments, the predictor variable is the knocked-down gene, while the other genes are potential targets. It can also be used for differential expression/2-class data.

r-txdb-hsapiens-ucsc-hg38-knowngene 3.22.0
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.hg38.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 hg38 genome and based on the "knownGene" track. The database is exposed as a TxDb object.

r-champdata 2.42.0
Propagated dependencies: r-biocgenerics@0.56.0 r-genomicranges@1.62.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ChAMPdata
Licenses: GPL 3
Build system: r
Synopsis: Data packages for ChAMP package
Description:

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

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