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r-tximportdata 1.40.0
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-scannotatr 1.18.0
Propagated dependencies: r-annotationhub@4.2.0 r-ape@5.8-1 r-caret@7.0-1 r-data-tree@1.2.0 r-dplyr@1.2.1 r-e1071@1.7-17 r-ggplot2@4.0.3 r-kernlab@0.9-33 r-proc@1.19.0.1 r-rocr@1.0-12 r-seurat@5.5.0 r-singlecellexperiment@1.34.0 r-summarizedexperiment@1.42.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/grisslab/scAnnotatR
Licenses: Expat
Build system: r
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-affycompatible 1.58.0
Propagated dependencies: r-biostrings@2.80.1 r-rcurl@1.98-1.18 r-xml@3.99-0.23
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AffyCompatible/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Work with Affymetrix GeneChip files
Description:

This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. It also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.

r-bsgenome 1.80.0
Propagated dependencies: r-biocgenerics@0.58.1 r-biocio@1.22.0 r-biostrings@2.80.1 r-genomicranges@1.64.0 r-iranges@2.46.0 r-matrixstats@1.5.0 r-rsamtools@2.28.0 r-rtracklayer@1.72.0 r-s4vectors@0.50.1 r-seqinfo@1.2.0 r-xvector@0.52.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BSgenome
Licenses: Artistic License 2.0
Build system: r
Synopsis: Infrastructure for Biostrings-based genome data packages
Description:

This package provides infrastructure shared by all Biostrings-based genome data packages and support for efficient SNP representation.

r-scds 2.0.0
Propagated dependencies: r-dplyr@1.2.1 r-matrix@1.7-5 r-proc@1.19.0.1 r-s4vectors@0.50.1 r-singlecellexperiment@1.34.0 r-summarizedexperiment@1.42.0 r-xgboost@3.2.1.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/scds
Licenses: Expat
Build system: r
Synopsis: In-silico doublet annotation for single cell RNA sequencing data
Description:

This is an R package for doublet annotation of single cell RNA sequencing data. scds provides methods to annotate doublets in scRNA-seq data computationally.

r-fcscan 1.26.0
Propagated dependencies: r-doparallel@1.0.17 r-foreach@1.5.2 r-genomicranges@1.64.0 r-iranges@2.46.0 r-plyr@1.8.9 r-rtracklayer@1.72.0 r-summarizedexperiment@1.42.0 r-variantannotation@1.58.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/fcScan
Licenses: Artistic License 2.0
Build system: r
Synopsis: Detect clusters of coordinates with user defined options
Description:

This package is used to detect combination of genomic coordinates falling within a user defined window size along with user defined overlap between identified neighboring clusters. It can be used for genomic data where the clusters are built on a specific chromosome or specific strand. Clustering can be performed with a "greedy" option allowing thus the presence of additional sites within the allowed window size.

r-biocio 1.22.0
Propagated dependencies: r-biocgenerics@0.58.1 r-s4vectors@0.50.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BiocIO
Licenses: Artistic License 2.0
Build system: r
Synopsis: Standard input and output for Bioconductor packages
Description:

This package implements `import()` and `export()` standard generics for importing and exporting biological data formats. `import()` supports whole-file as well as chunk-wise iterative import. The `import()` interface optionally provides a standard mechanism for 'lazy' access via `filter()` (on row or element-like components of the file resource), `select()` (on column-like components of the file resource) and `collect()`. The `import()` interface optionally provides transparent access to remote (e.g. via https) as well as local access. Developers can register a file extension, e.g., `.loom` for dispatch from character-based URIs to specific `import()` / `export()` methods based on classes representing file types, e.g., `LoomFile()`.

r-wrench 1.30.0
Propagated dependencies: r-limma@3.68.3 r-locfit@1.5-9.12 r-matrixstats@1.5.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/HCBravoLab/Wrench
Licenses: Artistic License 2.0
Build system: r
Synopsis: Wrench normalization for sparse count data
Description:

Wrench is a package for normalization sparse genomic count data, like that arising from 16s metagenomic surveys.

r-ggm 2.5.2
Propagated dependencies: r-biocmanager@1.30.27 r-graph@1.90.0 r-igraph@2.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://cran.r-project.org/package=ggm
Licenses: GPL 2+
Build system: r
Synopsis: Functions for graphical Markov models
Description:

This package provides functions and datasets for maximum likelihood fitting of some classes of graphical Markov models.

r-asset 2.30.0
Propagated dependencies: r-mass@7.3-65 r-msm@1.8.2 r-rmeta@3.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ASSET
Licenses: GPL 2
Build system: r
Synopsis: Subset-based association analysis of heterogeneous traits and subtypes
Description:

This package is an R program for the subset-based analysis of heterogeneous traits and disease subtypes. ASSET allows the user to search through all possible subsets of z-scores to identify the subset of traits giving the best meta-analyzed z-score. Further, it returns a p-value adjusting for the multiple-testing involved in the search. It also allows for searching for the best combination of disease subtypes associated with each variant.

r-adamgui 1.28.0
Propagated dependencies: r-adam@1.28.0 r-colorramps@2.3.4 r-data-table@1.18.4 r-dplyr@1.2.1 r-dt@0.34.0 r-ggplot2@4.0.3 r-ggpubr@0.6.3 r-ggrepel@0.9.8 r-ggsignif@0.6.4 r-go-db@3.23.1 r-gridextra@2.3 r-knitr@1.51 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-shiny@1.13.0 r-shinyjs@2.1.1 r-stringi@1.8.7 r-stringr@1.6.0 r-testthat@3.3.2 r-varhandle@2.0.6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ADAMgui/
Licenses: GPL 2+
Build system: r
Synopsis: GUI for gene activity and diversity analysis
Description:

This package ADAMgui is a graphical user interface (GUI) for the ADAM package. The ADAMgui package provides two shiny-based applications that allows the user to study the output of the ADAM package files through different plots. It's possible, for example, to choose a specific group of functionally associated genes (GFAG) and observe the gene expression behavior with the plots created with the GFAGtargetUi function. Features such as differential expression and fold change can be easily seen with aid of the plots made with the GFAGpathUi function.

r-flowutils 1.59.0
Propagated dependencies: r-biobase@2.72.0 r-corpcor@1.6.10 r-flowcore@2.24.0 r-graph@1.90.0 r-runit@0.4.33.1 r-xml@3.99-0.23
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/jspidlen/flowUtils
Licenses: Artistic License 2.0
Build system: r
Synopsis: Utilities for flow cytometry
Description:

This package provides utilities for flow cytometry data.

r-rots 2.4.0
Propagated dependencies: r-biobase@2.72.0 r-biocparallel@1.46.0 r-lme4@2.0-1 r-rcpp@1.1.1-1.1 r-survival@3.8-6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ROTS/
Licenses: GPL 2+
Build system: r
Synopsis: Reproducibility-Optimized Test Statistic
Description:

This package provides tools for calculating the Reproducibility-Optimized Test Statistic (ROTS) for differential testing in omics data.

r-grohmm 1.46.0
Propagated dependencies: r-genomicalignments@1.48.0 r-genomicranges@1.64.0 r-iranges@2.46.0 r-mass@7.3-65 r-rtracklayer@1.72.0 r-s4vectors@0.50.1 r-seqinfo@1.2.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/Kraus-Lab/groHMM
Licenses: GPL 3+
Build system: r
Synopsis: GRO-seq analysis pipeline
Description:

This package provides a pipeline for the analysis of GRO-seq data.

r-classdiscovery 3.4.9
Propagated dependencies: r-biobase@2.72.0 r-cluster@2.1.8.2 r-mclust@6.1.2 r-oompabase@3.2.11 r-oompadata@3.1.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://oompa.r-forge.r-project.org/
Licenses: ASL 2.0
Build system: r
Synopsis: Classes and methods for "Class Discovery" with Microarrays or Proteomics
Description:

This package defines classes for "class discovery" in the OOMPA project. Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance.

r-yaqcaffy 1.50.0
Propagated dependencies: r-simpleaffy@2.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/yaqcaffy/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix quality control and reproducibility analysis
Description:

This is a package that can be used for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.

r-clusterexperiment 2.32.0
Propagated dependencies: r-ape@5.8-1 r-biocgenerics@0.58.1 r-biocsingular@1.28.0 r-cluster@2.1.8.2 r-delayedarray@0.38.1 r-edger@4.10.0 r-hdf5array@1.40.0 r-kernlab@0.9-33 r-limma@3.68.3 r-locfdr@1.1-8 r-matrix@1.7-5 r-matrixstats@1.5.0 r-mbkmeans@1.28.0 r-nmf@0.28 r-phylobase@0.8.12 r-pracma@2.4.6 r-rcolorbrewer@1.1-3 r-rcpp@1.1.1-1.1 r-s4vectors@0.50.1 r-scales@1.4.0 r-singlecellexperiment@1.34.0 r-stringr@1.6.0 r-summarizedexperiment@1.42.0 r-zinbwave@1.34.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/clusterExperiment/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Compare clusterings for single-cell sequencing
Description:

This package provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA expression data sets.

r-convert 1.88.0
Propagated dependencies: r-biobase@2.72.0 r-limma@3.68.3 r-marray@1.90.0
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-mfuzz 2.72.0
Propagated dependencies: r-biobase@2.72.0 r-e1071@1.7-17 r-tkwidgets@1.90.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://mfuzz.sysbiolab.eu/
Licenses: GPL 2
Build system: r
Synopsis: Soft clustering of time series gene expression data
Description:

This is a package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface).

r-alabaster-se 1.12.0
Propagated dependencies: r-alabaster-base@1.12.0 r-alabaster-matrix@1.12.0 r-alabaster-ranges@1.12.0 r-biocgenerics@0.58.1 r-genomicranges@1.64.0 r-iranges@2.46.0 r-jsonlite@2.0.0 r-s4vectors@0.50.1 r-summarizedexperiment@1.42.0
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-genomicfiles 1.48.0
Propagated dependencies: r-biocbaseutils@1.14.0 r-biocgenerics@0.58.1 r-biocparallel@1.46.0 r-genomeinfodb@1.48.0 r-genomicalignments@1.48.0 r-genomicranges@1.64.0 r-iranges@2.46.0 r-matrixgenerics@1.24.0 r-rsamtools@2.28.0 r-rtracklayer@1.72.0 r-s4vectors@0.50.1 r-seqinfo@1.2.0 r-summarizedexperiment@1.42.0 r-variantannotation@1.58.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GenomicFiles
Licenses: Artistic License 2.0
Build system: r
Synopsis: Distributed computing by file or by range
Description:

This package provides infrastructure for parallel computations distributed by file or by range. User defined mapper and reducer functions provide added flexibility for data combination and manipulation.

r-chipexoqual 1.36.0
Propagated dependencies: r-biocparallel@1.46.0 r-biovizbase@1.60.0 r-broom@1.0.13 r-data-table@1.18.4 r-dplyr@1.2.1 r-genomicalignments@1.48.0 r-genomicranges@1.64.0 r-ggplot2@4.0.3 r-hexbin@1.28.5 r-iranges@2.46.0 r-rcolorbrewer@1.1-3 r-rmarkdown@2.31 r-rsamtools@2.28.0 r-s4vectors@0.50.1 r-scales@1.4.0 r-seqinfo@1.2.0 r-viridis@0.6.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/keleslab/ChIPexoQual
Licenses: GPL 2+
Build system: r
Synopsis: Quality control pipeline for ChIP-exo/nexus data
Description:

This package provides a quality control pipeline for ChIP-exo/nexus sequencing data.

r-decoupler 2.17.0
Propagated dependencies: r-biocparallel@1.46.0 r-broom@1.0.13 r-dplyr@1.2.1 r-magrittr@2.0.5 r-matrix@1.7-5 r-parallelly@1.47.0 r-purrr@1.2.2 r-rlang@1.2.0 r-stringr@1.6.0 r-tibble@3.3.1 r-tidyr@1.3.2 r-tidyselect@1.2.1 r-withr@3.0.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://saezlab.github.io/decoupleR/
Licenses: GPL 3
Build system: r
Synopsis: Computational methods to infer biological activities from omics data
Description:

Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. decoupleR is a Bioconductor package containing different statistical methods to extract these signatures within a unified framework. decoupleR allows the user to flexibly test any method with any resource. It incorporates methods that take into account the sign and weight of network interactions. decoupleR can be used with any omic, as long as its features can be linked to a biological process based on prior knowledge. For example, in transcriptomics gene sets regulated by a transcription factor, or in phospho-proteomics phosphosites that are targeted by a kinase.

r-tcgabiolinksgui-data 1.32.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI.data
Licenses: GPL 3
Build system: r
Synopsis: Data for the TCGAbiolinksGUI package
Description:

This package provides supporting data for the TCGAbiolinksGUI package.

Total packages: 72465