_            _    _        _         _
      /\ \         /\ \ /\ \     /\_\      / /\
      \_\ \       /  \ \\ \ \   / / /     / /  \
      /\__ \     / /\ \ \\ \ \_/ / /     / / /\ \__
     / /_ \ \   / / /\ \ \\ \___/ /     / / /\ \___\
    / / /\ \ \ / / /  \ \_\\ \ \_/      \ \ \ \/___/
   / / /  \/_// / /   / / / \ \ \        \ \ \
  / / /      / / /   / / /   \ \ \   _    \ \ \
 / / /      / / /___/ / /     \ \ \ /_/\__/ / /
/_/ /      / / /____\/ /       \ \_\\ \/___/ /
\_\/       \/_________/         \/_/ \_____\/

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.

If you'd like to join our channel webring send a patch to ~whereiseveryone/toys@lists.sr.ht adding your channel as an entry in channels.scm.


r-donapllp2013 1.48.0
Propagated dependencies: r-ebimage@4.52.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DonaPLLP2013
Licenses: Artistic License 2.0
Build system: r
Synopsis: Supplementary data package for Dona et al. (2013) containing example images and tables
Description:

An experiment data package associated with the publication Dona et al. (2013). Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics.

r-davidtiling 1.50.0
Propagated dependencies: r-tilingarray@1.88.0 r-go-db@3.22.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: http://www.ebi.ac.uk/huber
Licenses: LGPL 2.0+
Build system: r
Synopsis: Data and analysis scripts for David, Huber et al. yeast tiling array paper
Description:

This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory.

r-despace 2.2.2
Propagated dependencies: r-terra@1.8-86 r-summarizedexperiment@1.40.0 r-spatstat-geom@3.6-1 r-spatstat-explore@3.6-0 r-spatialexperiment@1.20.0 r-sf@1.0-23 r-scuttle@1.20.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-patchwork@1.3.2 r-matrix@1.7-4 r-limma@3.66.0 r-ggplot2@4.0.1 r-ggnewscale@0.5.2 r-ggforce@0.5.0 r-edger@4.8.0 r-dplyr@1.1.4 r-data-table@1.17.8 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-assertthat@0.2.1
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://github.com/peicai/DESpace
Licenses: GPL 3
Build system: r
Synopsis: DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions
Description:

Intuitive framework for identifying spatially variable genes (SVGs) and differential spatial variable pattern (DSP) between conditions via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. For multi-sample, multi-condition datasets, we again fit a NB model via edgeR, incorporating spatial clusters, conditions and their interactions as covariates. DSP genes-representing differences in spatial gene expression patterns across experimental conditions-are identified by testing the interaction between spatial clusters and conditions.

r-ddct 1.66.0
Propagated dependencies: r-xtable@1.8-4 r-rcolorbrewer@1.1-3 r-lattice@0.22-7 r-biocgenerics@0.56.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/ddCt
Licenses: LGPL 3
Build system: r
Synopsis: The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
Description:

The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.

r-dvddata 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DvDdata
Licenses: GPL 3
Build system: r
Synopsis: Drug versus Disease Data
Description:

Data package which provides default drug and disease expression profiles for the DvD package.

r-deedeeexperiment 1.0.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-limma@3.66.0 r-edger@4.8.0 r-deseq2@1.50.2 r-cli@3.6.5
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://github.com/imbeimainz/DeeDeeExperiment
Licenses: Expat
Build system: r
Synopsis: DeeDeeExperiment: An S4 Class for managing and exploring omics analysis results
Description:

DeeDeeExperiment is an S4 class extending the SingleCellExperiment class, designed to integrate and manage omics analysis results. It introduces two dedicated slots to store Differential Expression Analysis (DEA) results and Functional Enrichment Analysis (FEA) results, providing a structured approach for downstream analysis.

r-degseq 1.64.0
Propagated dependencies: r-qvalue@2.42.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DEGseq
Licenses: FSDG-compatible
Build system: r
Synopsis: Identify Differentially Expressed Genes from RNA-seq data
Description:

DEGseq is an R package to identify differentially expressed genes from RNA-Seq data.

r-dnabarcodecompatibility 1.26.0
Propagated dependencies: r-tidyr@1.3.1 r-stringr@1.6.0 r-rcpp@1.1.0 r-purrr@1.2.0 r-numbers@0.9-2 r-dplyr@1.1.4 r-bh@1.87.0-1
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://dnabarcodecompatibility.pasteur.fr/
Licenses: FSDG-compatible
Build system: r
Synopsis: Tool for Optimizing Combinations of DNA Barcodes Used in Multiplexed Experiments on Next Generation Sequencing Platforms
Description:

The package allows one to obtain optimised combinations of DNA barcodes to be used for multiplex sequencing. In each barcode combination, barcodes are pooled with respect to Illumina chemistry constraints. Combinations can be filtered to keep those that are robust against substitution and insertion/deletion errors thereby facilitating the demultiplexing step. In addition, the package provides an optimiser function to further favor the selection of barcode combinations with least heterogeneity in barcode usage.

r-dmchmm 1.32.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-multcomp@1.4-29 r-iranges@2.44.0 r-genomicranges@1.62.0 r-fdrtool@1.2.18 r-calibrate@1.7.7 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DMCHMM
Licenses: GPL 3
Build system: r
Synopsis: Differentially Methylated CpG using Hidden Markov Model
Description:

This package provides a pipeline for identifying differentially methylated CpG sites using Hidden Markov Model in bisulfite sequencing data. DNA methylation studies have enabled researchers to understand methylation patterns and their regulatory roles in biological processes and disease. However, only a limited number of statistical approaches have been developed to provide formal quantitative analysis. Specifically, a few available methods do identify differentially methylated CpG (DMC) sites or regions (DMR), but they suffer from limitations that arise mostly due to challenges inherent in bisulfite sequencing data. These challenges include: (1) that read-depths vary considerably among genomic positions and are often low; (2) both methylation and autocorrelation patterns change as regions change; and (3) CpG sites are distributed unevenly. Furthermore, there are several methodological limitations: almost none of these tools is capable of comparing multiple groups and/or working with missing values, and only a few allow continuous or multiple covariates. The last of these is of great interest among researchers, as the goal is often to find which regions of the genome are associated with several exposures and traits. To tackle these issues, we have developed an efficient DMC identification method based on Hidden Markov Models (HMMs) called “DMCHMM” which is a three-step approach (model selection, prediction, testing) aiming to address the aforementioned drawbacks.

r-dinor 1.6.0
Propagated dependencies: r-tidyselect@1.2.1 r-tidyr@1.3.1 r-tibble@3.3.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-rlang@1.1.6 r-matrix@1.7-4 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-edger@4.8.0 r-dplyr@1.1.4 r-cowplot@1.2.0 r-complexheatmap@2.26.0 r-circlize@0.4.16 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://github.com/xxxmichixxx/dinoR
Licenses: Expat
Build system: r
Synopsis: Differential NOMe-seq analysis
Description:

dinoR tests for significant differences in NOMe-seq footprints between two conditions, using genomic regions of interest (ROI) centered around a landmark, for example a transcription factor (TF) motif. This package takes NOMe-seq data (GCH methylation/protection) in the form of a Ranged Summarized Experiment as input. dinoR can be used to group sequencing fragments into 3 or 5 categories representing characteristic footprints (TF bound, nculeosome bound, open chromatin), plot the percentage of fragments in each category in a heatmap, or averaged across different ROI groups, for example, containing a common TF motif. It is designed to compare footprints between two sample groups, using edgeR's quasi-likelihood methods on the total fragment counts per ROI, sample, and footprint category.

r-dnazoodata 1.10.0
Propagated dependencies: r-s4vectors@0.48.0 r-rjson@0.2.23 r-hicexperiment@1.10.0 r-biocfilecache@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://github.com/js2264/DNAZooData
Licenses: Expat
Build system: r
Synopsis: DNA Zoo data package
Description:

DNAZooData is a data package giving programmatic access to genome assemblies and Hi-C contact matrices uniformly processed by the [DNA Zoo Consortium](https://www.dnazoo.org/). The matrices are available in the multi-resolution `.hic` format. A URL to corrected genome assemblies in `.fastq` format is also provided to the end-user.

r-demand 1.40.0
Propagated dependencies: r-kernsmooth@2.23-26
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DeMAND
Licenses: FSDG-compatible
Build system: r
Synopsis: DeMAND
Description:

DEMAND predicts Drug MoA by interrogating a cell context specific regulatory network with a small number (N >= 6) of compound-induced gene expression signatures, to elucidate specific proteins whose interactions in the network is dysregulated by the compound.

r-drosgenome1-db 3.13.0
Propagated dependencies: r-org-dm-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/drosgenome1.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix DrosGenome1 Array annotation data (chip drosgenome1)
Description:

Affymetrix Affymetrix DrosGenome1 Array annotation data (chip drosgenome1) assembled using data from public repositories.

r-dyebias 1.70.0
Propagated dependencies: r-marray@1.88.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: http://www.holstegelab.nl/publications/margaritis_lijnzaad
Licenses: GPL 3
Build system: r
Synopsis: The GASSCO method for correcting for slide-dependent gene-specific dye bias
Description:

Many two-colour hybridizations suffer from a dye bias that is both gene-specific and slide-specific. The former depends on the content of the nucleotide used for labeling; the latter depends on the labeling percentage. The slide-dependency was hitherto not recognized, and made addressing the artefact impossible. Given a reasonable number of dye-swapped pairs of hybridizations, or of same vs. same hybridizations, both the gene- and slide-biases can be estimated and corrected using the GASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009), doi:10.1038/msb.2009.21).

r-demixt 1.26.0
Propagated dependencies: r-truncdist@1.0-2 r-sva@3.58.0 r-summarizedexperiment@1.40.0 r-rmarkdown@2.30 r-rcpp@1.1.0 r-psych@2.5.6 r-matrixstats@1.5.0 r-matrixcalc@1.0-6 r-knitr@1.50 r-kernsmooth@2.23-26 r-ggplot2@4.0.1 r-dss@2.58.0 r-dendextend@1.19.1 r-base64enc@0.1-3
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DeMixT
Licenses: GPL 3
Build system: r
Synopsis: Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
Description:

DeMixT is a software package that performs deconvolution on transcriptome data from a mixture of two or three components.

r-delayeddataframe 1.26.0
Propagated dependencies: r-s4vectors@0.48.0 r-delayedarray@0.36.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://github.com/Bioconductor/DelayedDataFrame
Licenses: GPL 3
Build system: r
Synopsis: Delayed operation on DataFrame using standard DataFrame metaphor
Description:

Based on the standard DataFrame metaphor, we are trying to implement the feature of delayed operation on the DelayedDataFrame, with a slot of lazyIndex, which saves the mapping indexes for each column of DelayedDataFrame. Methods like show, validity check, [/[[ subsetting, rbind/cbind are implemented for DelayedDataFrame to be operated around lazyIndex. The listData slot stays untouched until a realization call e.g., DataFrame constructor OR as.list() is invoked.

r-doremitra 1.0.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-scater@1.38.0 r-s4vectors@0.48.0 r-glue@1.8.0 r-experimenthub@3.0.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://github.com/AhmedSAHassan/DoReMiTra
Licenses: Expat
Build system: r
Synopsis: Orchestrating Blood Radiation Transcriptomic Data
Description:

DoReMiTra is an R data package providing access to curated transcriptomic datasets related to blood radiation, with a focus on neutron, x-ray, and gamma ray studies. It is designed to facilitate radiation biology research and support data exploration and reproducibility in radiation transcriptomics. All datasets are provided as SummarizedExperiment objects, allowing seamless integration with the Bioconductor ecosystem.

r-depinfer 1.14.0
Propagated dependencies: r-matrixstats@1.5.0 r-glmnet@4.1-10 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DepInfeR
Licenses: GPL 3
Build system: r
Synopsis: Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling
Description:

DepInfeR integrates two experimentally accessible input data matrices: the drug sensitivity profiles of cancer cell lines or primary tumors ex-vivo (X), and the drug affinities of a set of proteins (Y), to infer a matrix of molecular protein dependencies of the cancers (ß). DepInfeR deconvolutes the protein inhibition effect on the viability phenotype by using regularized multivariate linear regression. It assigns a “dependence coefficient” to each protein and each sample, and therefore could be used to gain a causal and accurate understanding of functional consequences of genomic aberrations in a heterogeneous disease, as well as to guide the choice of pharmacological intervention for a specific cancer type, sub-type, or an individual patient. For more information, please read out preprint on bioRxiv: https://doi.org/10.1101/2022.01.11.475864.

r-drugvsdiseasedata 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DrugVsDiseasedata
Licenses: GPL 3
Build system: r
Synopsis: Drug versus Disease Data
Description:

Data package which provides default disease expression profiles, clusters and annotation information for use with the DrugVsDisease package.

r-dfp 1.68.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DFP
Licenses: GPL 2
Build system: r
Synopsis: Gene Selection
Description:

This package provides a supervised technique able to identify differentially expressed genes, based on the construction of \emphFuzzy Patterns (FPs). The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values.

r-dcats 1.8.0
Propagated dependencies: r-robustbase@0.99-6 r-mcmcpack@1.7-1 r-matrixstats@1.5.0 r-e1071@1.7-16 r-aod@1.3.3
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DCATS
Licenses: Expat
Build system: r
Synopsis: Differential Composition Analysis Transformed by a Similarity matrix
Description:

This package provides methods to detect the differential composition abundances between conditions in singel-cell RNA-seq experiments, with or without replicates. It aims to correct bias introduced by missclaisification and enable controlling of confounding covariates. To avoid the influence of proportion change from big cell types, DCATS can use either total cell number or specific reference group as normalization term.

r-deltacapturec 1.24.0
Propagated dependencies: r-tictoc@1.2.1 r-summarizedexperiment@1.40.0 r-iranges@2.44.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-deseq2@1.50.2
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/deltaCaptureC
Licenses: Expat
Build system: r
Synopsis: This Package Discovers Meso-scale Chromatin Remodeling from 3C Data
Description:

This package discovers meso-scale chromatin remodelling from 3C data. 3C data is local in nature. It givens interaction counts between restriction enzyme digestion fragments and a preferred viewpoint region. By binning this data and using permutation testing, this package can test whether there are statistically significant changes in the interaction counts between the data from two cell types or two treatments.

r-dune 1.22.0
Propagated dependencies: r-tidyr@1.3.1 r-summarizedexperiment@1.40.0 r-rcolorbrewer@1.1-3 r-purrr@1.2.0 r-magrittr@2.0.4 r-ggplot2@4.0.1 r-gganimate@1.0.11 r-dplyr@1.1.4 r-biocparallel@1.44.0 r-aricode@1.0.3
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/Dune
Licenses: Expat
Build system: r
Synopsis: Improving replicability in single-cell RNA-Seq cell type discovery
Description:

Given a set of clustering labels, Dune merges pairs of clusters to increase mean ARI between labels, improving replicability.

r-dmrcatedata 2.28.0
Propagated dependencies: r-rtracklayer@1.70.0 r-readxl@1.4.5 r-plyr@1.8.9 r-illuminahumanmethylationepicanno-ilm10b4-hg19@0.6.0 r-illuminahumanmethylation450kanno-ilmn12-hg19@0.6.1 r-gviz@1.54.0 r-genomicfeatures@1.62.0 r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/DMRcatedata
Licenses: GPL 3
Build system: r
Synopsis: Data Package for DMRcate
Description:

This package contains 9 data objects supporting functionality and examples of the Bioconductor package DMRcate.

Total results: 2909