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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.

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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-hitc 1.54.0
Propagated dependencies: r-biostrings@2.78.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-matrix@1.7-4 r-rcolorbrewer@1.1-3 r-rtracklayer@1.70.0 r-seqinfo@1.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/HiTC
Licenses: Artistic License 2.0
Build system: r
Synopsis: High throughput chromosome conformation capture analysis
Description:

The HiTC package was developed to explore high-throughput "C" data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.

r-minfidata 0.56.0
Propagated dependencies: r-illuminahumanmethylation450kanno-ilmn12-hg19@0.6.1 r-illuminahumanmethylation450kmanifest@0.4.0 r-minfi@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/minfiData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Example data for the Illumina Methylation 450k array
Description:

This package provides data from 6 samples across 2 groups from 450k methylation arrays.

r-rgadem 2.55.0
Propagated dependencies: r-biostrings@2.78.0 r-bsgenome@1.78.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-seqlogo@1.76.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/rGADEM/
Licenses: Artistic License 2.0
Build system: r
Synopsis: De novo sequence motif discovery
Description:

rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data.

r-gseabase 1.72.0
Propagated dependencies: r-annotate@1.88.0 r-annotationdbi@1.72.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-graph@1.88.0 r-xml@3.99-0.20
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/GSEABase
Licenses: Artistic License 2.0
Build system: r
Synopsis: Gene set enrichment data structures and methods
Description:

This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).

r-rtcgatoolbox 2.40.0
Propagated dependencies: r-biocgenerics@0.56.0 r-data-table@1.17.8 r-delayedarray@0.36.0 r-genomicranges@1.62.0 r-httr@1.4.7 r-raggedexperiment@1.34.0 r-rcurl@1.98-1.17 r-rjsonio@2.0.0 r-rvest@1.0.5 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-tcgautils@1.30.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://mksamur.github.io/RTCGAToolbox/
Licenses: GPL 2
Build system: r
Synopsis: Export TCGA Firehose data
Description:

Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. This package provides an extensible R based data client for Firehose pre-processed data.

r-rbowtie2 2.16.0
Dependencies: samtools@1.19
Propagated dependencies: r-magrittr@2.0.4 r-rsamtools@2.26.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Rbowtie2/
Licenses: GPL 3+
Build system: r
Synopsis: R wrapper for Bowtie2 and AdapterRemoval
Description:

This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging.

r-affyplm 1.86.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-affy@1.88.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-gcrma@2.82.0 r-preprocesscore@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/bmbolstad/affyPLM
Licenses: GPL 2+
Build system: r
Synopsis: Methods for fitting probe-level models
Description:

The affyPLM provides a package that extends and improves the functionality of the base affy package. For speeding up the runs, it includes routines that make heavy use of compiled code. The central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools are also provided.

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-abarray 1.78.0
Propagated dependencies: r-biobase@2.70.0 r-multtest@2.66.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ABarray
Licenses: GPL 2+
Build system: r
Synopsis: Gene expression analysis for Applied Biosystems Genome Survey Microarray
Description:

The package ABarray is designed to work with Applied Biosystems whole genome microarray platform, as well as any other platform whose data can be transformed into expression data matrix. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A graphical user interface (GUI) is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used.

r-degreport 1.46.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-broom@1.0.10 r-circlize@0.4.16 r-cluster@2.1.8.1 r-complexheatmap@2.26.0 r-consensusclusterplus@1.74.0 r-cowplot@1.2.0 r-dendextend@1.19.1 r-deseq2@1.50.2 r-dplyr@1.1.4 r-edger@4.8.0 r-ggdendro@0.2.0 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-knitr@1.50 r-logging@0.10-108 r-magrittr@2.0.4 r-psych@2.5.6 r-rcolorbrewer@1.1-3 r-reshape@0.8.10 r-rlang@1.1.6 r-s4vectors@0.48.0 r-scales@1.4.0 r-stringi@1.8.7 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-tibble@3.3.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://lpantano.github.io/DEGreport/
Licenses: Expat
Build system: r
Synopsis: Report of DEG analysis
Description:

This is a package for creating na HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.

r-affyrnadegradation 1.56.0
Propagated dependencies: r-affy@1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AffyRNADegradation
Licenses: GPL 2+
Build system: r
Synopsis: Analyze and correct probe positional bias in data due to RNA degradation
Description:

The AffyRNADegradation package helps with the assessment and correction of RNA degradation effects in Affymetrix 3 expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.

r-biscuiteer 1.24.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biscuiteerdata@1.24.0 r-bsseq@1.46.0 r-data-table@1.17.8 r-delayedmatrixstats@1.32.0 r-dmrseq@1.30.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-gtools@3.9.5 r-hdf5array@1.38.0 r-homo-sapiens@1.3.1 r-impute@1.84.0 r-iranges@2.44.0 r-matrix@1.7-4 r-matrixstats@1.5.0 r-mus-musculus@1.3.1 r-qdnaseq@1.46.0 r-qualv@0.3-5 r-r-utils@2.13.0 r-readr@2.1.6 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/trichelab/biscuiteer
Licenses: GPL 3
Build system: r
Synopsis: Convenience functions for the Biscuit package
Description:

This package provides a test harness for bsseq loading of Biscuit output, summarization of WGBS data over defined regions and in mappable samples, with or without imputation, dropping of mostly-NA rows, age estimates, etc.

r-timeseriesexperiment 1.13.0
Propagated dependencies: r-deseq2@1.50.2 r-dplyr@1.1.4 r-dynamictreecut@1.63-1 r-edger@4.8.0 r-ggplot2@4.0.1 r-hmisc@5.2-4 r-limma@3.66.0 r-magrittr@2.0.4 r-proxy@0.4-27 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-vegan@2.7-2 r-viridis@0.6.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/nlhuong/TimeSeriesExperiment/
Licenses: LGPL 3+
Build system: r
Synopsis: Analysis for short time-series data
Description:

This package is a visualization and analysis toolbox for short time course data which includes dimensionality reduction, clustering, two-sample differential expression testing and gene ranking techniques. The package also provides methods for retrieving enriched pathways.

r-annotationfuncs 1.40.0
Propagated dependencies: r-annotationdbi@1.72.0 r-dbi@1.2.3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.iysik.com/r/annotationfuncs
Licenses: GPL 2
Build system: r
Synopsis: Annotation translation functions
Description:

This package provides functions for handling translating between different identifieres using the Biocore Data Team data-packages (e.g. org.Bt.eg.db).

r-genomationdata 1.42.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioinformatics.mdc-berlin.de/genomation/
Licenses: GPL 3+
Build system: r
Synopsis: Experimental data for use with the genomation package
Description:

This package contains experimental genetic data for use with the genomation package. Included are Chip Seq, Methylation and Cage data, downloaded from Encode.

r-do-db 2.9
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/DO.db/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation maps describing the entire Disease Ontology
Description:

This package provides a set of annotation maps describing the entire Disease Ontology.

r-immapex 1.4.0
Propagated dependencies: r-hash@2.2.6.3 r-httr@1.4.7 r-matrix@1.7-4 r-matrixstats@1.5.0 r-rcpp@1.1.0 r-rvest@1.0.5 r-singlecellexperiment@1.32.0 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/BorchLab/immApex/
Licenses: Expat
Build system: r
Synopsis: Adaptive immune receptor sequence-based machine and deep learning
Description:

This package provides a set of tools to for machine and deep learning in R from amino acid and nucleotide sequences focusing on adaptive immune receptors. The package includes pre-processing of sequences, unifying gene nomenclature usage, encoding sequences, and combining models. This package will serve as the basis of future immune receptor sequence functions/packages/models compatible with the scRepertoire ecosystem.

r-bsgenome-drerio-ucsc-danrer7 1.4.0
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.danRer7
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Danio rerio (UCSC version danRer7)
Description:

This package provides full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects.

r-wppi 1.16.0
Propagated dependencies: r-dplyr@1.1.4 r-igraph@2.2.1 r-logger@0.4.1 r-magrittr@2.0.4 r-matrix@1.7-4 r-omnipathr@3.14.0 r-progress@1.2.3 r-purrr@1.2.0 r-rcurl@1.98-1.17 r-rlang@1.1.6 r-tibble@3.3.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/AnaGalhoz37/wppi
Licenses: Expat
Build system: r
Synopsis: Weighting protein-protein interactions
Description:

This package predicts functional relevance of protein-protein interactions based on functional annotations such as Human Protein Ontology and Gene Ontology, and prioritizes genes based on network topology, functional scores and a path search algorithm.

r-multibac 1.20.0
Propagated dependencies: r-ggplot2@4.0.1 r-matrix@1.7-4 r-multiassayexperiment@1.36.1 r-pcamethods@2.2.0 r-plotrix@3.8-13 r-ropls@1.42.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MultiBaC
Licenses: GPL 3
Build system: r
Synopsis: Multiomic batch effect correction
Description:

MultiBaC is a strategy to correct batch effects from multiomic datasets distributed across different labs or data acquisition events. MultiBaC is able to remove batch effects across different omics generated within separate batches provided that at least one common omic data type is included in all the batches considered.

r-plgem 1.82.0
Propagated dependencies: r-biobase@2.70.0 r-mass@7.3-65
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.genopolis.it
Licenses: GPL 2
Build system: r
Synopsis: Detect differential expression in microarray and proteomics datasets
Description:

The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use of PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets.

r-a4classif 1.58.0
Propagated dependencies: r-a4core@1.58.0 r-a4preproc@1.58.0 r-biobase@2.70.0 r-glmnet@4.1-10 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
Build system: r
Synopsis: Automated Affymetrix array analysis classification package
Description:

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

r-bionero 1.18.0
Propagated dependencies: r-biocparallel@1.44.0 r-complexheatmap@2.26.0 r-dynamictreecut@1.63-1 r-genie3@1.32.0 r-ggdendro@0.2.0 r-ggnetwork@0.5.14 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-igraph@2.2.1 r-intergraph@2.0-4 r-matrixstats@1.5.0 r-minet@3.68.0 r-netrep@1.2.9 r-patchwork@1.3.2 r-rcolorbrewer@1.1-3 r-reshape2@1.4.5 r-rlang@1.1.6 r-summarizedexperiment@1.40.0 r-sva@3.58.0 r-wgcna@1.73
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/almeidasilvaf/BioNERO
Licenses: GPL 3
Build system: r
Synopsis: Biological network reconstruction omnibus
Description:

BioNERO aims to integrate all aspects of biological network inference in a single package, including data preprocessing, exploratory analyses, network inference, and analyses for biological interpretations. BioNERO can be used to infer gene coexpression networks (GCNs) and gene regulatory networks (GRNs) from gene expression data. Additionally, it can be used to explore topological properties of protein-protein interaction (PPI) networks. GCN inference relies on the popular WGCNA algorithm. GRN inference is based on the "wisdom of the crowds" principle, which consists in inferring GRNs with multiple algorithms (here, CLR, GENIE3 and ARACNE) and calculating the average rank for each interaction pair. As all steps of network analyses are included in this package, BioNERO makes users avoid having to learn the syntaxes of several packages and how to communicate between them. Finally, users can also identify consensus modules across independent expression sets and calculate intra and interspecies module preservation statistics between different networks.

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