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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-rnbeads-hg38 1.42.1
Propagated dependencies: r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RnBeads.hg38
Licenses: GPL 3
Build system: r
Synopsis: RnBeads.hg38
Description:

RnBeads annotation package for the assembly hg38.

r-rat2302cdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rat2302cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: rat2302cdf
Description:

This package provides a package containing an environment representing the Rat230_2.cdf file.

r-rgu34ccdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rgu34ccdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: rgu34ccdf
Description:

This package provides a package containing an environment representing the RG_U34C.cdf file.

r-rigraphlib 1.2.0
Propagated dependencies: r-biocmake@1.2.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/libscran/Rigraphlib
Licenses: GPL 3
Build system: r
Synopsis: igraph library as an R package
Description:

Vendors the igraph C source code and builds it into a static library. Other Bioconductor packages can link to libigraph.a in their own C/C++ code. This is intended for packages wrapping C/C++ libraries that depend on the igraph C library and cannot be easily adapted to use the igraph R package.

r-rbwa 1.14.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/Jfortin1/Rbwa
Licenses: Expat
Build system: r
Synopsis: R wrapper for BWA-backtrack and BWA-MEM aligners
Description:

This package provides an R wrapper for BWA alignment algorithms. Both BWA-backtrack and BWA-MEM are available. Convenience function to build a BWA index from a reference genome is also provided. Currently not supported for Windows machines.

r-rnaseqpower 1.50.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RNASeqPower
Licenses: FSDG-compatible
Build system: r
Synopsis: Sample size for RNAseq studies
Description:

RNA-seq, sample size.

r-rmagpie 1.66.0
Propagated dependencies: r-pamr@1.57 r-kernlab@0.9-33 r-e1071@1.7-16 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://www.bioconductor.org/
Licenses: GPL 3+
Build system: r
Synopsis: MicroArray Gene-expression-based Program In Error rate estimation
Description:

Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. A range of modern classifiers are available, including support vector machines (SVMs), nearest shrunken centroids (NSCs)... Advanced methods are provided to estimate the predictive error rate and to report the subset of genes which appear essential in discriminating between classes.

r-rsweep 1.22.0
Propagated dependencies: r-stringi@1.8.7 r-foreach@1.5.2 r-doparallel@1.0.17 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rSWeeP
Licenses: GPL 2+
Build system: r
Synopsis: Spaced Words Projection (SWeeP)
Description:

"Spaced Words Projection (SWeeP)" is a method for representing biological sequences using vectors preserving inter-sequence comparability.

r-rmmquant 1.28.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-txdb-mmusculus-ucsc-mm9-knowngene@3.2.2 r-tbx20bamsubset@1.46.0 r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rcpp@1.1.0 r-org-mm-eg-db@3.22.0 r-genomicranges@1.62.0 r-devtools@2.4.6 r-deseq2@1.50.2 r-biocstyle@2.38.0 r-apeglm@1.32.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/Rmmquant
Licenses: GPL 3
Build system: r
Synopsis: RNA-Seq multi-mapping Reads Quantification Tool
Description:

RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used, but all of them provide biased results. With Rmmquant, if a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Rmmquant is a drop-in replacement of the widely used tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased way.

r-rae230bcdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rae230bcdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: rae230bcdf
Description:

This package provides a package containing an environment representing the RAE230B.CDF file.

r-rvs 1.32.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RVS
Licenses: GPL 2
Build system: r
Synopsis: Computes estimates of the probability of related individuals sharing a rare variant
Description:

Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).

r-ruvnormalize 1.44.0
Propagated dependencies: r-ruvnormalizedata@1.30.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RUVnormalize
Licenses: GPL 3
Build system: r
Synopsis: RUV for normalization of expression array data
Description:

RUVnormalize is meant to remove unwanted variation from gene expression data when the factor of interest is not defined, e.g., to clean up a dataset for general use or to do any kind of unsupervised analysis.

r-rlmm 1.72.0
Propagated dependencies: r-mass@7.3-65
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://www.stat.berkeley.edu/users/nrabbee/RLMM
Licenses: LGPL 2.0+
Build system: r
Synopsis: Genotype Calling Algorithm for Affymetrix SNP Arrays
Description:

This package provides a classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.

r-redseq 1.56.0
Propagated dependencies: r-multtest@2.66.0 r-iranges@2.44.0 r-chippeakanno@3.44.0 r-bsgenome-celegans-ucsc-ce2@1.4.0 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocgenerics@0.56.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/REDseq
Licenses: FSDG-compatible
Build system: r
Synopsis: Analysis of high-throughput sequencing data processed by restriction enzyme digestion
Description:

The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.

r-rae230acdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rae230acdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: rae230acdf
Description:

This package provides a package containing an environment representing the RAE230A.CDF file.

r-rocpai 1.22.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-knitr@1.50 r-fission@1.30.0 r-boot@1.3-32
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/ROCpAI
Licenses: GPL 3
Build system: r
Synopsis: Receiver Operating Characteristic Partial Area Indexes for evaluating classifiers
Description:

The package analyzes the Curve ROC, identificates it among different types of Curve ROC and calculates the area under de curve through the method that is most accuracy. This package is able to standarizate proper and improper pAUC.

r-recountmethylation 1.20.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/metamaden/recountmethylation
Licenses: Artistic License 2.0
Build system: r
Synopsis: Access and analyze public DNA methylation array data compilations
Description:

Resources for cross-study analyses of public DNAm array data from NCBI GEO repo, produced using Illumina's Infinium HumanMethylation450K (HM450K) and MethylationEPIC (EPIC) platforms. Provided functions enable download, summary, and filtering of large compilation files. Vignettes detail background about file formats, example analyses, and more. Note the disclaimer on package load and consult the main manuscripts for further info.

r-ribosomeprofilingqc 1.22.0
Propagated dependencies: r-xvector@0.50.0 r-txdbmaker@1.6.0 r-seqinfo@1.0.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-ruvseq@1.44.0 r-rtracklayer@1.70.0 r-rsubread@2.24.0 r-rsamtools@2.26.0 r-motifstack@1.54.0 r-iranges@2.44.0 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-ggfittext@0.10.2 r-ggextra@0.11.0 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomicalignments@1.46.0 r-genomeinfodb@1.46.0 r-edaseq@2.44.0 r-cluster@2.1.8.1 r-bsgenome@1.78.0 r-biostrings@2.78.0 r-biocgenerics@0.56.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/ribosomeProfilingQC
Licenses: FSDG-compatible
Build system: r
Synopsis: Ribosome Profiling Quality Control
Description:

Ribo-Seq (also named ribosome profiling or footprinting) measures translatome (unlike RNA-Seq, which sequences the transcriptome) by direct quantification of the ribosome-protected fragments (RPFs). This package provides the tools for quality assessment of ribosome profiling. In addition, it can preprocess Ribo-Seq data for subsequent differential analysis.

r-rgsepd 1.42.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-org-hs-eg-db@3.22.0 r-gplots@3.2.0 r-goseq@1.62.0 r-go-db@3.22.0 r-deseq2@1.50.2 r-biomart@2.66.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rgsepd
Licenses: GPL 3
Build system: r
Synopsis: Gene Set Enrichment / Projection Displays
Description:

R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at transcript IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.

r-rnamodr-ml 1.24.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://github.com/FelixErnst/RNAmodR.ML
Licenses: Artistic License 2.0
Build system: r
Synopsis: Detecting patterns of post-transcriptional modifications using machine learning
Description:

RNAmodR.ML extend the functionality of the RNAmodR package and classical detection strategies towards detection through machine learning models. RNAmodR.ML provides classes, functions and an example workflow to establish a detection stratedy, which can be packaged.

r-rebet 1.28.0
Propagated dependencies: r-asset@2.28.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/REBET
Licenses: GPL 2
Build system: r
Synopsis: The subREgion-based BurdEn Test (REBET)
Description:

There is an increasing focus to investigate the association between rare variants and diseases. The REBET package implements the subREgion-based BurdEn Test which is a powerful burden test that simultaneously identifies susceptibility loci and sub-regions.

r-rgu34bprobe 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/rgu34bprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type rgu34b
Description:

This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RG-U34B\_probe\_tab.

r-rtcga-methylation 1.38.0
Propagated dependencies: r-rtcga@1.40.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: https://bioconductor.org/packages/RTCGA.methylation
Licenses: GPL 2
Build system: r
Synopsis: Methylation datasets from The Cancer Genome Atlas Project
Description:

Package provides methylation (humanmethylation27) datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/DNA+methylation Data from 2015-11-01 snapshot.

r-rcellminer 2.32.0
Propagated dependencies: r-stringr@1.6.0 r-shiny@1.11.1 r-rcellminerdata@2.32.0 r-gplots@3.2.0 r-ggplot2@4.0.1 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/r.scm (guix-bioc packages r)
Home page: http://discover.nci.nih.gov/cellminer/
Licenses: FSDG-compatible
Build system: r
Synopsis: rcellminer: Molecular Profiles, Drug Response, and Chemical Structures for the NCI-60 Cell Lines
Description:

The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.

Total results: 2911