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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-tkwidgets 1.88.0
Propagated dependencies: r-dyndoc@1.88.0 r-widgettools@1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/tkWidgets
Licenses: Artistic License 2.0
Build system: r
Synopsis: R based tk widgets
Description:

This package implements widgets to provide user interfaces.

r-arrayexpress 1.70.0
Propagated dependencies: r-biobase@2.70.0 r-httr@1.4.7 r-jsonlite@2.0.0 r-limma@3.66.0 r-oligo@1.74.0 r-rlang@1.1.6
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ArrayExpress
Licenses: Artistic License 2.0
Build system: r
Synopsis: Building R objects from ArrayExpress datasets
Description:

This package offers the possibility to access the ArrayExpress repository at EBI (European Bioinformatics Institute) and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet.

r-hdf5array 1.38.0
Propagated dependencies: r-biocgenerics@0.56.0 r-delayedarray@0.36.0 r-h5mread@1.2.0 r-iranges@2.44.0 r-matrix@1.7-4 r-rhdf5@2.54.0 r-s4arrays@1.10.0 r-s4vectors@0.48.0 r-sparsearray@1.10.2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/HDF5Array
Licenses: Artistic License 2.0
Build system: r
Synopsis: HDF5 back end for DelayedArray objects
Description:

This package provides an array-like container for convenient access and manipulation of HDF5 datasets. It supports delayed operations and block processing.

r-biocgenerics 0.56.0
Propagated dependencies: r-generics@0.1.4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BiocGenerics
Licenses: Artistic License 2.0
Build system: r
Synopsis: S4 generic functions for Bioconductor
Description:

This package provides S4 generic functions needed by many Bioconductor packages.

r-riboprofiling 1.39.1
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-data-table@1.17.8 r-genomicalignments@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-ggbio@1.58.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-plyr@1.8.9 r-reshape2@1.4.5 r-rsamtools@2.26.0 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-sqldf@0.4-11
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/RiboProfiling/
Licenses: GPL 3
Build system: r
Synopsis: Ribosome profiling data analysis
Description:

Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.

r-flowutils 1.59.0
Propagated dependencies: r-biobase@2.70.0 r-corpcor@1.6.10 r-flowcore@2.22.0 r-graph@1.88.0 r-runit@0.4.33.1 r-xml@3.99-0.20
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-amplican 1.32.1
Propagated dependencies: r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biostrings@2.78.0 r-cluster@2.1.8.1 r-data-table@1.17.8 r-dplyr@1.1.4 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-ggthemes@5.1.0 r-gridextra@2.3 r-gtable@0.3.6 r-iranges@2.44.0 r-knitr@1.50 r-matrix@1.7-4 r-matrixstats@1.5.0 r-pwalign@1.6.0 r-rcpp@1.1.0 r-rmarkdown@2.30 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-shortread@1.68.0 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/valenlab/amplican
Licenses: GPL 3
Build system: r
Synopsis: Automated analysis of CRISPR experiments
Description:

The package performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents the results in the form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.

r-debcam 1.26.0
Dependencies: openjdk@11.0.22 java-pj@20150107
Propagated dependencies: r-apcluster@1.4.14 r-biobase@2.70.0 r-biocparallel@1.44.0 r-corpcor@1.6.10 r-dmwr2@0.0.2 r-geometry@0.5.2 r-nmf@0.28 r-nnls@1.6 r-pcapp@2.0-5 r-rjava@1.0-11 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/debCAM
Licenses: GPL 2
Build system: r
Synopsis: Deconvolution by convex analysis of mixtures
Description:

This package is an R implementation for fully unsupervised deconvolution of complex tissues. DebCAM provides basic functions to perform unsupervised deconvolution on mixture expression profiles by CAM and some auxiliary functions to help understand the subpopulation- specific results. It also implements functions to perform supervised deconvolution based on prior knowledge of molecular markers, S matrix or A matrix. Combining molecular markers from CAM and from prior knowledge can achieve semi-supervised deconvolution of mixtures.

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-biobroom 1.42.0
Propagated dependencies: r-biobase@2.70.0 r-broom@1.0.10 r-dplyr@1.1.4 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/StoreyLab/biobroom
Licenses: LGPL 3+
Build system: r
Synopsis: Turn Bioconductor objects into tidy data frames
Description:

This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.

r-snplocs-hsapiens-dbsnp144-grch37 0.99.20
Propagated dependencies: r-biocgenerics@0.56.0 r-bsgenome@1.78.0 r-genomeinfodb@1.46.0 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://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/
Licenses: Artistic License 2.0
Build system: r
Synopsis: SNP locations for Homo sapiens (dbSNP Build 144)
Description:

This package provides SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be injected in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).

r-gwascat 2.42.0
Propagated dependencies: r-annotationdbi@1.72.0 r-annotationhub@4.0.0 r-biocfilecache@3.0.0 r-biostrings@2.78.0 r-data-table@1.17.8 r-genomeinfodb@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-iranges@2.44.0 r-readr@2.1.6 r-s4vectors@0.48.0 r-seqinfo@1.0.0 r-snpstats@1.60.0 r-tibble@3.3.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/gwascat
Licenses: Artistic License 2.0
Build system: r
Synopsis: Tools for data in the EMBL-EBI GWAS catalog
Description:

This package provides tools for representing and modeling data in the EMBL-EBI GWAS catalog.

r-isoformswitchanalyzer 2.10.0
Propagated dependencies: r-biobase@2.70.0 r-biocgenerics@0.56.0 r-biocparallel@1.44.0 r-biostrings@2.78.0 r-bsgenome@1.78.0 r-dbi@1.2.3 r-dexseq@1.56.0 r-dplyr@1.1.4 r-edger@4.8.0 r-futile-logger@1.4.3 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-gridextra@2.3 r-iranges@2.44.0 r-limma@3.66.0 r-magrittr@2.0.4 r-pfamanalyzer@1.10.0 r-plyr@1.8.9 r-pwalign@1.6.0 r-rcolorbrewer@1.1-3 r-rcurl@1.98-1.17 r-readr@2.1.6 r-reshape2@1.4.5 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-saturn@1.18.0 r-seqinfo@1.0.0 r-stringr@1.6.0 r-summarizedexperiment@1.40.0 r-sva@3.58.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-tximeta@1.28.0 r-tximport@1.38.1 r-venndiagram@1.7.3 r-xvector@0.50.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/IsoformSwitchAnalyzeR/
Licenses: GPL 2+
Build system: r
Synopsis: Analyze alternative splicing in RNA-seq data
Description:

This is a package for the analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.

r-annaffy 1.82.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biobase@2.70.0 r-biocmanager@1.30.27 r-dbi@1.2.3 r-go-db@3.22.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/annaffy/
Licenses: LGPL 2.1+
Build system: r
Synopsis: Annotation tools for Affymetrix biological metadata
Description:

This package provides functions for handling data from Bioconductor Affymetrix annotation data packages. It produces compact HTML and text reports including experimental data and URL links to many online databases. It allows searching of biological metadata using various criteria.

r-abadata 1.12.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/ABAData/
Licenses: GPL 2+
Build system: r
Synopsis: Gene expression in human brain regions from Allen Brain Atlas
Description:

This package provides the data for the gene expression enrichment analysis conducted in the package ABAEnrichment. The package includes three datasets which are derived from the Allen Brain Atlas:

  1. Gene expression data from Human Brain (adults) averaged across donors,

  2. Gene expression data from the Developing Human Brain pooled into five age categories and averaged across donors, and

  3. a developmental effect score based on the Developing Human Brain expression data.

All datasets are restricted to protein coding genes.

r-experimenthub 3.0.0
Propagated dependencies: r-annotationhub@4.0.0 r-biocfilecache@3.0.0 r-biocgenerics@0.56.0 r-biocmanager@1.30.27 r-rappdirs@0.3.3 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ExperimentHub/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Client to access ExperimentHub resources
Description:

This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.

r-flowsorted-blood-450k 1.48.0
Propagated dependencies: r-minfi@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/FlowSorted.Blood.450k
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina HumanMethylation data on sorted blood cell populations
Description:

This package provides raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type.

r-cardelino 1.12.0
Propagated dependencies: r-combinat@0.0-8 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-ggtree@4.0.1 r-matrix@1.7-4 r-matrixstats@1.5.0 r-pheatmap@1.0.13 r-s4vectors@0.48.0 r-snpstats@1.60.0 r-variantannotation@1.56.0 r-vcfr@1.15.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/single-cell-genetics/cardelino
Licenses: GPL 3
Build system: r
Synopsis: Clone identification from single cell data
Description:

This package provides methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stochastic dropout events as well as systematic allelic imbalance is used.

r-epidish 2.26.0
Propagated dependencies: r-e1071@1.7-16 r-locfdr@1.1-8 r-mass@7.3-65 r-matrix@1.7-4 r-matrixstats@1.5.0 r-quadprog@1.5-8 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/sjczheng/EpiDISH
Licenses: GPL 2
Build system: r
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-protgear 1.14.0
Propagated dependencies: r-biobase@2.70.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-factoextra@1.0.7 r-factominer@2.12 r-flexdashboard@0.6.2 r-genefilter@1.92.0 r-ggally@2.4.0 r-ggplot2@4.0.1 r-ggpubr@0.6.2 r-gtools@3.9.5 r-htmltools@0.5.8.1 r-kendall@2.2.1 r-knitr@1.50 r-limma@3.66.0 r-magrittr@2.0.4 r-mass@7.3-65 r-pheatmap@1.0.13 r-plotly@4.11.0 r-plyr@1.8.9 r-purrr@1.2.0 r-readr@2.1.6 r-remotes@2.5.0 r-rlang@1.1.6 r-rmarkdown@2.30 r-shiny@1.11.1 r-shinydashboard@0.7.3 r-styler@1.11.0 r-tibble@3.3.0 r-tidyr@1.3.1 r-vsn@3.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/Keniajin/protGear
Licenses: GPL 3
Build system: r
Synopsis: Protein micro array data management and interactive visualization
Description:

This package provides a generic three-step pre-processing package for protein microarray data. This package contains different data pre-processing procedures to allow comparison of their performance. These steps are background correction, the coefficient of variation (CV) based filtering, batch correction and normalization.

r-mafdb-1kgenomes-phase1-hs37d5 3.10.0
Propagated dependencies: r-bsgenome@1.78.0 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-genomicscores@2.22.0 r-iranges@2.44.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/MafDb.1Kgenomes.phase1.hs37d5
Licenses: Artistic License 2.0
Build system: r
Synopsis: Minor allele frequency data from 1000 Genomes Phase 1 for hs37d5
Description:

Store minor allele frequency data from the Phase 1 of the 1000 Genomes Project for the human genome version hs37d5.

r-seqinfo 1.0.0
Propagated dependencies: r-biocgenerics@0.56.0 r-iranges@2.44.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/Seqinfo
Licenses: Artistic License 2.0
Build system: r
Synopsis: S4 class for storing basic information about a collection of genomic sequences
Description:

The Seqinfo class stores the names, lengths, circularity flags, and genomes for a particular collection of sequences. These sequences are typically the chromosomes and/or scaffolds of a specific genome assembly of a given organism. Seqinfo objects are rarely used as standalone objects. Instead, they are used as part of higher-level objects to represent their seqinfo() component. Examples of such higher-level objects are GRanges, RangedSummarizedExperiment, VCF, GAlignments, etc… defined in other Bioconductor infrastructure packages.

r-affycoretools 1.82.0
Propagated dependencies: r-affy@1.88.0 r-annotationdbi@1.72.0 r-biobase@2.70.0 r-biocgenerics@0.56.0 r-dbi@1.2.3 r-edger@4.8.0 r-gcrma@2.82.0 r-ggplot2@4.0.1 r-glimma@2.20.0 r-gostats@2.76.0 r-gplots@3.2.0 r-hwriter@1.3.2.1 r-lattice@0.22-7 r-limma@3.66.0 r-oligoclasses@1.72.0 r-reportingtools@2.50.0 r-rsqlite@2.4.4 r-s4vectors@0.48.0 r-xtable@1.8-4
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/affycoretools/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Functions for analyses with Affymetrix GeneChips
Description:

This package provides various wrapper functions that have been written to streamline the more common analyses that a Biostatistician might see.

r-baalchip 1.36.0
Propagated dependencies: r-coda@0.19-4.1 r-doby@4.7.0 r-doparallel@1.0.17 r-foreach@1.5.2 r-genomeinfodb@1.46.0 r-genomicalignments@1.46.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-reshape2@1.4.5 r-rsamtools@2.26.0 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/BaalChIP
Licenses: Artistic License 2.0
Build system: r
Synopsis: Analysis of allele-specific transcription factor binding in cancer genomes
Description:

This package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. It computes allele counts at individual variants (SNPs/SNVs), implements extensive QC (quality control) steps to remove problematic variants, and utilizes a Bayesian framework to identify statistically significant allele-specific events. BaalChIP is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples.

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