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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.

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r-amountain 1.36.0
Dependencies: gsl@2.8
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/AMOUNTAIN
Licenses: GPL 2+
Build system: r
Synopsis: Modules for multilayer weighted gene co-expression networks
Description:

This package provides a pure data-driven gene network, WGCN(weighted gene co-expression network) could be constructed only from expression profile. Different layers in such networks may represent different time points, multiple conditions or various species. AMOUNTAIN aims to search active modules in multi-layer WGCN using a continuous optimization approach.

r-deconvr 1.16.0
Propagated dependencies: r-assertthat@0.2.1 r-biocgenerics@0.56.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-e1071@1.7-16 r-foreach@1.5.2 r-genomicranges@1.62.0 r-iranges@2.44.0 r-magrittr@2.0.4 r-mass@7.3-65 r-matrixstats@1.5.0 r-methylkit@1.36.0 r-minfi@1.56.0 r-nnls@1.6 r-quadprog@1.5-8 r-rsq@2.7 r-s4vectors@0.48.0 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/BIMSBbioinfo/deconvR
Licenses: Artistic License 2.0
Build system: r
Synopsis: Simulation and deconvolution of omic profiles
Description:

This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types. The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally, we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.

r-lfa 2.10.0
Propagated dependencies: r-corpcor@1.6.10 r-rspectra@0.16-2
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/StoreyLab/lfa
Licenses: GPL 3
Build system: r
Synopsis: Logistic Factor Analysis for categorical data
Description:

Logistic Factor Analysis (LFA) is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter.

r-arrmdata 1.46.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/ARRmData/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Example dataset for normalization of Illumina 450k methylation data
Description:

This package provides raw beta values from 36 samples across 3 groups from Illumina 450k methylation arrays.

r-bsgenome-hsapiens-1000genomes-hs37d5 0.99.1
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Homo sapiens
Description:

This package provides full genome sequences for Homo sapiens from 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.

r-metaneighbor 1.29.0
Propagated dependencies: r-beanplot@1.3.1 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-gplots@3.2.0 r-igraph@2.2.1 r-matrix@1.7-4 r-matrixstats@1.5.0 r-rcolorbrewer@1.1-3 r-singlecellexperiment@1.32.0 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://bioconductor.org/packages/MetaNeighbor
Licenses: Expat
Build system: r
Synopsis: Single cell replicability analysis
Description:

This package implements a method to rapidly assess cell type identity using both functional and random gene sets and it allows users to quantify cell type replicability across datasets using neighbor voting. MetaNeighbor works on the basis that cells of the same type should have more similar gene expression profiles than cells of different types.

r-dmrseq 1.30.0
Propagated dependencies: r-annotationhub@4.0.0 r-annotatr@1.36.0 r-biocparallel@1.44.0 r-bsseq@1.46.0 r-bumphunter@1.52.0 r-delayedmatrixstats@1.32.0 r-genomicranges@1.62.0 r-ggplot2@4.0.1 r-iranges@2.44.0 r-locfit@1.5-9.12 r-matrixstats@1.5.0 r-nlme@3.1-168 r-outliers@0.15 r-rcolorbrewer@1.1-3 r-rtracklayer@1.70.0 r-s4vectors@0.48.0 r-seqinfo@1.0.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/dmrseq
Licenses: Expat
Build system: r
Synopsis: Detection and inference of differentially methylated regions
Description:

This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution, that can be implemented even when as few as two samples per population are available. Region-level statistics are obtained by fitting a generalized least squares (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.

r-depecher 1.26.0
Propagated dependencies: r-beanplot@1.3.1 r-clusterr@1.3.5 r-collapse@2.1.5 r-dosnow@1.0.20 r-dplyr@1.1.4 r-fnn@1.1.4.1 r-foreach@1.5.2 r-ggplot2@4.0.1 r-gmodels@2.19.1 r-gplots@3.2.0 r-mass@7.3-65 r-matrixstats@1.5.0 r-mixomics@6.34.0 r-moments@0.14.1 r-rcpp@1.1.0 r-rcppeigen@0.3.4.0.2 r-reshape2@1.4.5 r-robustbase@0.99-6 r-viridis@0.6.5
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/DepecheR/
Licenses: Expat
Build system: r
Synopsis: Identify traits of clusters in high-dimensional entities
Description:

The purpose of this package is to identify traits in a dataset that can separate groups. This is done on two levels. First, clustering is performed, using an implementation of sparse K-means. Secondly, the generated clusters are used to predict outcomes of groups of individuals based on their distribution of observations in the different clusters. As certain clusters with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.

r-bandits 1.26.0
Propagated dependencies: r-biocparallel@1.44.0 r-data-table@1.17.8 r-doparallel@1.0.17 r-dorng@1.8.6.2 r-drimseq@1.38.0 r-foreach@1.5.2 r-ggplot2@4.0.1 r-mass@7.3-65 r-r-utils@2.13.0 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/SimoneTiberi/BANDITS
Licenses: GPL 3+
Build system: r
Synopsis: Bayesian analysis of differential splicing
Description:

BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via DTU (differential transcript usage), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via MCMC (Markov chain Monte Carlo) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts.

r-alpine 1.26.0
Propagated dependencies: 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-graph@1.88.0 r-iranges@2.44.0 r-rbgl@1.86.0 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-speedglm@0.3-5 r-stringr@1.6.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/alpine
Licenses: GPL 2+
Build system: r
Synopsis: Modeling and correcting fragment sequence bias
Description:

The package alpine helps to model bias parameters and then using those parameters to estimate RNA-seq transcript abundance. Alpine is a package for estimating and visualizing many forms of sample-specific biases that can arise in RNA-seq, including fragment length distribution, positional bias on the transcript, read start bias (random hexamer priming), and fragment GC-content (amplification). It also offers bias-corrected estimates of transcript abundance in FPKM(Fragments Per Kilobase of transcript per Million mapped reads). It is currently designed for un-stranded paired-end RNA-seq data.

r-bsgenome-celegans-ucsc-ce6 1.4.0
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full genome sequences for Worm
Description:

This package provides full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings objects.

r-rcistarget 1.29.0
Propagated dependencies: r-arrow@22.0.0 r-aucell@1.32.0 r-biocgenerics@0.56.0 r-data-table@1.17.8 r-dplyr@1.1.4 r-genomeinfodb@1.46.0 r-genomicranges@1.62.0 r-gseabase@1.72.0 r-r-utils@2.13.0 r-s4vectors@0.48.0 r-summarizedexperiment@1.40.0 r-tibble@3.3.0 r-zoo@1.8-14
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://aertslab.org/#scenic
Licenses: GPL 3
Build system: r
Synopsis: Identify transcription factor binding motifs enriched on a gene list
Description:

RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).

r-sangerseqr 1.46.0
Propagated dependencies: r-biostrings@2.78.0 r-pwalign@1.6.0 r-shiny@1.11.1 r-stringr@1.6.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/sangerseqR
Licenses: GPL 2
Build system: r
Synopsis: Tools for Sanger Sequencing data in R
Description:

This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms.

r-affydata 1.58.0
Propagated dependencies: r-affy@1.88.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/affydata/
Licenses: GPL 2+
Build system: r
Synopsis: Affymetrix data for demonstration purposes
Description:

This package provides example datasets that represent 'real world examples' of Affymetrix data, unlike the artificial examples included in the package affy.

r-aspli 2.20.0
Propagated dependencies: r-annotationdbi@1.72.0 r-biocgenerics@0.56.0 r-biocstyle@2.38.0 r-data-table@1.17.8 r-dt@0.34.0 r-edger@4.8.0 r-genomicalignments@1.46.0 r-genomicfeatures@1.62.0 r-genomicranges@1.62.0 r-gviz@1.54.0 r-htmltools@0.5.8.1 r-igraph@2.2.1 r-iranges@2.44.0 r-limma@3.66.0 r-mass@7.3-65 r-pbmcapply@1.5.1 r-rsamtools@2.26.0 r-s4vectors@0.48.0 r-tidyr@1.3.1 r-txdbmaker@1.6.0 r-upsetr@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/ASpli
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: Analysis of alternative splicing using RNA-Seq
Description:

AS (alternative splicing) is a common mechanism of post-transcriptional gene regulation in eukaryotic organisms that expands the functional and regulatory diversity of a single gene by generating multiple mRNA isoforms that encode structurally and functionally distinct proteins. ASpli is an integrative pipeline and user-friendly R package that facilitates the analysis of changes in both annotated and novel AS events. ASpli integrates several independent signals in order to deal with the complexity that might arise in splicing patterns.

r-msa 1.42.0
Propagated dependencies: r-biocgenerics@0.56.0 r-biostrings@2.78.0 r-iranges@2.44.0 r-rcpp@1.1.0 r-s4vectors@0.48.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: http://www.bioinf.jku.at/software/msa/
Licenses: GPL 2+
Build system: r
Synopsis: Multiple sequence alignment
Description:

The msa package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.

r-nebulosa 1.20.0
Propagated dependencies: r-ggplot2@4.0.1 r-ggrastr@1.0.2 r-ks@1.15.1 r-matrix@1.7-4 r-patchwork@1.3.2 r-seuratobject@5.2.0 r-singlecellexperiment@1.32.0 r-summarizedexperiment@1.40.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/powellgenomicslab/Nebulosa
Licenses: GPL 3
Build system: r
Synopsis: Single-cell data visualisation using kernel gene-weighted density estimation
Description:

This package provides a enhanced visualization of single-cell data based on gene-weighted density estimation. Nebulosa recovers the signal from dropped-out features and allows the inspection of the joint expression from multiple features (e.g. genes). Seurat and SingleCellExperiment objects can be used within Nebulosa.

r-zfpkm 1.32.0
Propagated dependencies: r-checkmate@2.3.3 r-dplyr@1.1.4 r-ggplot2@4.0.1 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/ronammar/zFPKM/
Licenses: GPL 3
Build system: r
Synopsis: Functions to facilitate zFPKM transformations
Description:

This is a package to perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113).

r-yapsa 1.36.0
Propagated dependencies: r-biostrings@2.78.0 r-bsgenome-hsapiens-ucsc-hg19@1.4.3 r-circlize@0.4.16 r-complexheatmap@2.26.0 r-corrplot@0.95 r-dendextend@1.19.1 r-doparallel@1.0.17 r-dplyr@1.1.4 r-genomicranges@1.62.0 r-getoptlong@1.0.5 r-ggbeeswarm@0.7.2 r-ggplot2@4.0.1 r-gridextra@2.3 r-gtrellis@1.42.0 r-keggrest@1.50.0 r-limsolve@2.0.1 r-magrittr@2.0.4 r-pmcmrplus@1.9.12 r-pracma@2.4.6 r-reshape2@1.4.5 r-seqinfo@1.0.0 r-somaticsignatures@2.46.0 r-variantannotation@1.56.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/YAPSA/
Licenses: GPL 3
Build system: r
Synopsis: Yet another package for signature analysis
Description:

This package provides functions and routines useful in the analysis of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, functions to perform a signature analysis with known signatures and a signature analysis on stratified mutational catalogue (SMC) are provided.

r-seqlogo 1.76.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://bioconductor.org/packages/seqLogo
Licenses: LGPL 2.0+
Build system: r
Synopsis: Sequence logos for DNA sequence alignments
Description:

seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).

r-maftools 2.26.0
Propagated dependencies: r-data-table@1.17.8 r-dnacopy@1.84.0 r-pheatmap@1.0.13 r-rcolorbrewer@1.1-3 r-rhtslib@3.6.0 r-survival@3.8-3
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/PoisonAlien/maftools
Licenses: Expat
Build system: r
Synopsis: Summarize, analyze and visualize MAF files
Description:

Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.

r-sanssouci 0-1.5fe20a9
Propagated dependencies: r-generics@0.1.4 r-matrix@1.7-4 r-matrixstats@1.5.0 r-rcpp@1.1.0 r-rcpparmadillo@15.2.2-1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://pneuvial.github.io/sanssouci
Licenses: GPL 3
Build system: r
Synopsis: Post Hoc multiple testing inference
Description:

The goal of sansSouci is to perform post hoc inference: in a multiple testing context, sansSouci provides statistical guarantees on possibly user-defined and/or data-driven sets of hypotheses.

r-fgsea 1.36.0
Propagated dependencies: r-bh@1.87.0-1 r-biocparallel@1.44.0 r-cowplot@1.2.0 r-data-table@1.17.8 r-fastmatch@1.1-6 r-ggplot2@4.0.1 r-matrix@1.7-4 r-rcpp@1.1.0 r-scales@1.4.0
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/ctlab/fgsea/
Licenses: Expat
Build system: r
Synopsis: Fast gene set enrichment analysis
Description:

The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm makes more permutations and gets more fine grained p-values, which allows using accurate standard approaches to multiple hypothesis correction.

r-progeny 1.32.0
Propagated dependencies: r-biobase@2.70.0 r-decoupler@2.16.0 r-dplyr@1.1.4 r-ggplot2@4.0.1 r-ggrepel@0.9.6 r-gridextra@2.3 r-reshape2@1.4.5 r-tidyr@1.3.1
Channel: guix
Location: gnu/packages/bioconductor.scm (gnu packages bioconductor)
Home page: https://github.com/saezlab/progeny
Licenses: ASL 2.0
Build system: r
Synopsis: Pathway responsive gene activity inference
Description:

This package provides a function to infer pathway activity from gene expression. It contains the linear model inferred in the publication "Perturbation-response genes reveal signaling footprints in cancer gene expression".

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