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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-chromstardata 1.36.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/chromstaRData/
Licenses: GPL 3
Build system: r
Synopsis: ChIP-seq data for demonstration purposes
Description:

This package provides ChIP-seq data for demonstration purposes in the chromstaR package.

r-imputelcmd 2.1
Propagated dependencies: r-impute@1.84.0 r-norm@1.0-11.1 r-pcamethods@2.2.0 r-tmvtnorm@1.7
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/package=imputeLCMD
Licenses: GPL 2+
Build system: r
Synopsis: Collection of methods for left-censored missing data imputation
Description:

This package provides a collection of functions for left-censored missing data imputation. Left-censoring is a special case of missing not at random (MNAR) mechanism that generates non-responses in proteomics experiments. The package also contains functions to artificially generate peptide/protein expression data (log-transformed) as random draws from a multivariate Gaussian distribution as well as a function to generate missing data (both randomly and non-randomly). For comparison reasons, the package also contains several wrapper functions for the imputation of non-responses that are missing at random.

r-affyilm 1.62.0
Propagated dependencies: r-affxparser@1.82.0 r-affy@1.88.0 r-biobase@2.70.0 r-gcrma@2.82.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/affyILM
Licenses: GPL 3
Build system: r
Synopsis: Linear model of background subtraction and the Langmuir isotherm
Description:

The affyILM package is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behal of the Langmuir model.

r-bcellviper 1.46.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/bcellViper
Licenses: GPL 2+
Build system: r
Synopsis: Transcriptional interactome and normal human B-cell expression data
Description:

This is a tool for human B-cell context-specific transcriptional regulatory network. In addition, this package provides a human normal B-cells dataset for the examples in package viper.

r-anvil 1.22.0
Propagated dependencies: r-anvilbase@1.4.0 r-biocbaseutils@1.12.0 r-dplyr@1.1.4 r-dt@0.34.0 r-futile-logger@1.4.3 r-gcptools@1.0.0 r-htmltools@0.5.8.1 r-httr@1.4.7 r-jsonlite@2.0.0 r-miniui@0.1.2 r-rapiclient@0.1.8 r-shiny@1.11.1 r-tibble@3.3.0 r-yaml@2.3.10
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AnVIL
Licenses: Artistic License 2.0
Build system: r
Synopsis: Provides access to AnVIL, Terra, Leonardo and other projects
Description:

The AnVIL is a cloud computing resource developed in part by the National Human Genome Research Institute. The AnVIL package provides end-user and developer functionality. AnVIL provides fast binary package installation, utilities for working with Terra/AnVIL table and data resources, and convenient functions for file movement to and from Google cloud storage. For developers, AnVIL provides programmatic access to the Terra, Leonardo, Rawls, Dockstore, and Gen3 RESTful programming interface, including helper functions to transform JSON responses to formats more amenable to manipulation in R.

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-metap 1.12
Propagated dependencies: r-lattice@0.22-7 r-mathjaxr@1.8-0 r-mutoss@0.1-13 r-qqconf@1.3.2 r-rdpack@2.6.4 r-tfisher@0.2.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://www.dewey.myzen.co.uk/meta/meta.html
Licenses: GPL 2
Build system: r
Synopsis: Meta-analysis of significance values
Description:

The canonical way to perform meta-analysis involves using effect sizes. When they are not available this package provides a number of methods for meta-analysis of significance values including the methods of Edgington, Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results; and a routine for graphical display.

r-biocparallel 1.44.0
Propagated dependencies: r-bh@1.87.0-1 r-codetools@0.2-20 r-cpp11@0.5.2 r-futile-logger@1.4.3 r-snow@0.4-4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BiocParallel
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: Bioconductor facilities for parallel evaluation
Description:

This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

r-deseq2 1.50.2
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-locfit@1.5-9.12 r-matrixgenerics@1.22.0 r-matrixstats@1.5.0 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1 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/DESeq2
Licenses: LGPL 3+
Build system: r
Synopsis: Differential gene expression analysis
Description:

This package provides functions to estimate variance-mean dependence in count data from high-throughput nucleotide sequencing assays and test for differential expression based on a model using the negative binomial distribution.

r-ggpicrust2 2.5.2
Propagated dependencies: r-aplot@0.2.9 r-dplyr@1.1.4 r-ggh4x@0.3.1 r-ggplot2@4.0.1 r-ggplotify@0.1.3 r-ggprism@1.0.7 r-ggraph@2.2.2 r-magrittr@2.0.4 r-patchwork@1.3.2 r-progress@1.2.3 r-readr@2.1.6 r-tibble@3.3.0 r-tidygraph@1.3.1 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/cafferychen777/ggpicrust2
Licenses: Expat
Build system: r
Synopsis: Make PICRUSt2 output analysis and visualization easier
Description:

This package provides a convenient way to analyze and visualize PICRUSt2 output with pre-defined plots and functions. It allows for generating statistical plots about microbiome functional predictions and offers customization options. It features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. It streamlines the PICRUSt2 analysis and visualization process.

r-decipher 3.6.0
Propagated dependencies: r-biostrings@2.78.0 r-dbi@1.2.3 r-iranges@2.44.0 r-s4vectors@0.48.0 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/DECIPHER/
Licenses: GPL 3
Build system: r
Synopsis: Tools for deciphering and managing biological sequences
Description:

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

r-makecdfenv 1.86.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-affy@1.88.0 r-affyio@1.80.0 r-biobase@2.70.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/makecdfenv
Licenses: GPL 2+
Build system: r
Synopsis: Chip description file environment maker
Description:

This package implements two functions. One of them reads an Affymetrix CDF and creates a hash table environment containing the location/probe set membership mapping. The other one creates a package that automatically loads that environment.

r-valr 0.8.4
Propagated dependencies: r-broom@1.0.10 r-cli@3.6.5 r-cpp11bigwig@0.1.2 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-lifecycle@1.0.4 r-rcpp@1.1.0 r-readr@2.1.6 r-rlang@1.1.6 r-stringr@1.6.0 r-tibble@3.3.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/rnabioco/valr
Licenses: Expat
Build system: r
Synopsis: Genome interval arithmetic in R
Description:

This package enables you to read and manipulate genome intervals and signals. It provides functionality similar to command-line tool suites within R, enabling interactive analysis and visualization of genome-scale data.

r-sgseq 1.44.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-igraph@2.2.1 r-iranges@2.44.0 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-runit@0.4.33.1 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/SGSeq/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Splice event prediction and quantification from RNA-seq data
Description:

SGSeq is a package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice graph, which can be obtained from existing annotation or predicted from the mapped sequence reads. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation.

r-cistopic-next 0.3.0-1.04cecbb
Propagated dependencies: r-aucell@1.32.0 r-data-table@1.17.8 r-dosnow@1.0.20 r-dplyr@1.1.4 r-dt@0.34.0 r-feather@0.3.5 r-fitdistrplus@1.2-4 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-lda@1.5.2 r-matrix@1.7-4 r-plyr@1.8.9 r-rcistarget@1.29.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-text2vec@0.6.4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/aertslab/cisTopic
Licenses: GPL 3
Build system: r
Synopsis: Modelling of cis-regulatory topics from single cell epigenomics data
Description:

The sparse nature of single cell epigenomics data can be overruled using probabilistic modelling methods such as Latent Dirichlet Allocation (LDA). This package allows the probabilistic modelling of cis-regulatory topics (cisTopics) from single cell epigenomics data, and includes functionalities to identify cell states based on the contribution of cisTopics and explore the nature and regulatory proteins driving them.

r-bags 2.50.0
Propagated dependencies: r-biobase@2.70.0 r-breastcancervdx@1.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BAGS
Licenses: Artistic License 2.0
Build system: r
Synopsis: Bayesian approach for geneset selection
Description:

This R package is providing functions to perform geneset significance analysis over simple cross-sectional data between 2 and 5 phenotypes of interest.

r-fastseg 1.56.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-s4vectors@0.48.0
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+
Build system: r
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-alabaster-se 1.10.0
Propagated dependencies: r-alabaster-base@1.10.0 r-alabaster-matrix@1.10.0 r-alabaster-ranges@1.10.0 r-biocgenerics@0.56.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-jsonlite@2.0.0 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/alabaster.se
Licenses: Expat
Build system: r
Synopsis: Load and save SummarizedExperiments from file
Description:

This is a package for saving SummarizedExperiments into file artifacts, and loading them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

r-dss 2.58.0
Propagated dependencies: r-biobase@2.70.0 r-biocparallel@1.44.0 r-bsseq@1.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/DSS
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: Dispersion shrinkage for sequencing data
Description:

DSS is an R library performing differential analysis for count-based sequencing data. It detects differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.

r-yarn 1.36.0
Propagated dependencies: r-biobase@2.70.0 r-biomart@2.66.0 r-downloader@0.4.1 r-edger@4.8.0 r-gplots@3.2.0 r-limma@3.66.0 r-matrixstats@1.5.0 r-preprocesscore@1.72.0 r-quantro@1.44.0 r-rcolorbrewer@1.1-3 r-readr@2.1.6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/yarn/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Robust multi-condition RNA-Seq preprocessing and normalization
Description:

Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.

r-bader 1.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BADER
Licenses: GPL 2
Build system: r
Synopsis: Bayesian analysis of differential expression in RNA sequencing data
Description:

The BADER package is intended for the analysis of RNA sequencing data. The algorithm fits a Bayesian hierarchical model for RNA sequencing count data. BADER returns the posterior probability of differential expression for each gene between two groups A and B. The joint posterior distribution of the variables in the model can be returned in the form of posterior samples, which can be used for further down-stream analyses such as gene set enrichment.

r-bsgenome-drerio-ucsc-danrer10 1.4.2
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BSgenome.Drerio.UCSC.danRer10
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Danio rerio (UCSC version danRer10)
Description:

This package provides full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer10, Sep. 2014) and stored in Biostrings objects.

r-biobase 2.70.0
Propagated dependencies: r-biocgenerics@0.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Biobase
Licenses: Artistic License 2.0
Build system: r
Synopsis: Base functions for Bioconductor
Description:

This package provides functions that are needed by many other packages on Bioconductor or which replace R functions.

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Total results: 69112