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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.

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-drosgenome1probe 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/drosgenome1probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type drosgenome1
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 DrosGenome1\_probe\_tab.

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-decontx 1.8.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://bioconductor.org/packages/decontX
Licenses: Expat
Build system: r
Synopsis: Decontamination of single cell genomics data
Description:

This package contains implementation of DecontX (Yang et al. 2020), a decontamination algorithm for single-cell RNA-seq, and DecontPro (Yin et al. 2023), a decontamination algorithm for single cell protein expression data. DecontX is a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. DecontPro is a Bayesian method that estimates the level of contamination from ambient and background sources in CITE-seq ADT dataset and decontaminate the dataset.

r-dandelionr 1.2.0
Channel: guix-bioc
Location: guix-bioc/packages/d.scm (guix-bioc packages d)
Home page: https://www.github.com/tuonglab/dandelionR/
Licenses: Expat
Build system: r
Synopsis: Single-cell Immune Repertoire Trajectory Analysis in R
Description:

dandelionR is an R package for performing single-cell immune repertoire trajectory analysis, based on the original python implementation. It provides the necessary functions to interface with scRepertoire and a custom implementation of an absorbing Markov chain for pseudotime inference, inspired by the Palantir Python package.

r-ensdb-rnorvegicus-v75 2.99.0
Propagated dependencies: r-ensembldb@2.34.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EnsDb.Rnorvegicus.v75
Licenses: Artistic License 2.0
Build system: r
Synopsis: Ensembl based annotation package
Description:

Exposes an annotation databases generated from Ensembl.

r-elvis 1.2.0
Propagated dependencies: r-zoo@1.8-14 r-uuid@1.2-1 r-txdbmaker@1.6.0 r-stringr@1.6.0 r-segclust2d@0.3.3 r-scales@1.4.0 r-reticulate@1.44.1 r-patchwork@1.3.2 r-memoise@2.0.1 r-magrittr@2.0.4 r-iranges@2.44.0 r-igraph@2.2.1 r-glue@1.8.0 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-dplyr@1.1.4 r-data-table@1.17.8 r-complexheatmap@2.26.0 r-circlize@0.4.16 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/hyochoi/ELViS
Licenses: Expat
Build system: r
Synopsis: An R Package for Estimating Copy Number Levels of Viral Genome Segments Using Base-Resolution Read Depth Profile
Description:

Base-resolution copy number analysis of viral genome. Utilizes base-resolution read depth data over viral genome to find copy number segments with two-dimensional segmentation approach. Provides publish-ready figures, including histograms of read depths, coverage line plots over viral genome annotated with copy number change events and viral genes, and heatmaps showing multiple types of data with integrative clustering of samples.

r-eopreddata 1.4.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/wvictor14/eoPredData
Licenses: Expat
Build system: r
Synopsis: ExperimentHub package containing model data for predicting preeclampsia status for based on plcaental DNA methylation profile
Description:

This package provides access to eoPred pretrained model hosted on ExperimentHub. Model was trained on placental DNA methylation preeclampsia samples using mixOmics splsda. There are two resources: 1. the model object, and 2. a testing data set used to demonstrate the function.

r-easycelltype 1.12.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EasyCellType
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotate cell types for scRNA-seq data
Description:

We developed EasyCellType which can automatically examine the input marker lists obtained from existing software such as Seurat over the cell markerdatabases. Two quantification approaches to annotate cell types are provided: Gene set enrichment analysis (GSEA) and a modified versio of Fisher's exact test. The function presents annotation recommendations in graphical outcomes: bar plots for each cluster showing candidate cell types, as well as a dot plot summarizing the top 5 significant annotations for each cluster.

r-encodexplorerdata 0.99.5
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/ENCODExplorerData
Licenses: Artistic License 2.0
Build system: r
Synopsis: compilation of ENCODE metadata
Description:

This package allows user to quickly access ENCODE project files metadata and give access to helper functions to query the ENCODE rest api, download ENCODE datasets and save the database in SQLite format.

r-excluderanges 0.99.10
Propagated dependencies: r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/dozmorovlab/excluderanges
Licenses: Expat
Build system: r
Synopsis: Genomic coordinates of problematic genomic regions
Description:

Genomic coordinates of problematic genomic regions that should be avoided when working with genomic data. GRanges of exclusion regions (formerly known as blacklisted), centromeres, telomeres, known heterochromatin regions, etc. (UCSC gap table data). Primarily for human and mouse genomes, hg19/hg38 and mm9/mm10 genome assemblies.

r-excluster 1.28.0
Propagated dependencies: r-rtracklayer@1.70.0 r-rsubread@2.24.0 r-matrixstats@1.5.0 r-iranges@2.44.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/ExCluster
Licenses: GPL 3
Build system: r
Synopsis: ExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition
Description:

ExCluster flattens Ensembl and GENCODE GTF files into GFF files, which are used to count reads per non-overlapping exon bin from BAM files. This read counting is done using the function featureCounts from the package Rsubread. Library sizes are normalized across all biological replicates, and ExCluster then compares two different conditions to detect signifcantly differentially spliced genes. This process requires at least two independent biological repliates per condition, and ExCluster accepts only exactly two conditions at a time. ExCluster ultimately produces false discovery rates (FDRs) per gene, which are used to detect significance. Exon log2 fold change (log2FC) means and variances may be plotted for each significantly differentially spliced gene, which helps scientists develop hypothesis and target differential splicing events for RT-qPCR validation in the wet lab.

r-experimentsubset 1.20.0
Propagated dependencies: r-treesummarizedexperiment@2.18.0 r-summarizedexperiment@1.40.0 r-spatialexperiment@1.20.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-matrix@1.7-4
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/ExperimentSubset
Licenses: Expat
Build system: r
Synopsis: Manages subsets of data with Bioconductor Experiment objects
Description:

Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for one or more matrix-like assays along with the associated row and column data. Often only a subset of the original data is needed for down-stream analysis. For example, filtering out poor quality samples will require excluding some columns before analysis. The ExperimentSubset object is a container to efficiently manage different subsets of the same data without having to make separate objects for each new subset.

r-egad 1.38.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EGAD
Licenses: GPL 2
Build system: r
Synopsis: Extending guilt by association by degree
Description:

The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods.

r-ewcedata 1.18.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/neurogenomics/ewceData
Licenses: Artistic License 2.0
Build system: r
Synopsis: The ewceData package provides reference data required for ewce
Description:

This package provides reference data required for ewce. Expression Weighted Celltype Enrichment (EWCE) is used to determine which cell types are enriched within gene lists. The package provides tools for testing enrichments within simple gene lists (such as human disease associated genes) and those resulting from differential expression studies. The package does not depend upon any particular Single Cell Transcriptome dataset and user defined datasets can be loaded in and used in the analyses.

r-eisar 1.22.1
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-limma@3.66.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-edger@4.8.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/fmicompbio/eisaR
Licenses: GPL 3
Build system: r
Synopsis: Exon-Intron Split Analysis (EISA) in R
Description:

Exon-intron split analysis (EISA) uses ordinary RNA-seq data to measure changes in mature RNA and pre-mRNA reads across different experimental conditions to quantify transcriptional and post-transcriptional regulation of gene expression. For details see Gaidatzis et al., Nat Biotechnol 2015. doi: 10.1038/nbt.3269. eisaR implements the major steps of EISA in R.

r-epimutacions 1.14.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/isglobal-brge/epimutacions
Licenses: Expat
Build system: r
Synopsis: Robust outlier identification for DNA methylation data
Description:

The package includes some statistical outlier detection methods for epimutations detection in DNA methylation data. The methods included in the package are MANOVA, Multivariate linear models, isolation forest, robust mahalanobis distance, quantile and beta. The methods compare a case sample with a suspected disease against a reference panel (composed of healthy individuals) to identify epimutations in the given case sample. It also contains functions to annotate and visualize the identified epimutations.

r-expressionatlas 2.2.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/ExpressionAtlas
Licenses: GPL 3+
Build system: r
Synopsis: Download datasets from EMBL-EBI Expression Atlas
Description:

This package is for searching for datasets in EMBL-EBI Expression Atlas, and downloading them into R for further analysis. Each Expression Atlas dataset is represented as a SimpleList object with one element per platform. Sequencing data is contained in a SummarizedExperiment object, while microarray data is contained in an ExpressionSet or MAList object.

r-emdomics 2.40.0
Propagated dependencies: r-preprocesscore@1.72.0 r-matrixstats@1.5.0 r-ggplot2@4.0.1 r-emdist@0.3-3 r-cdft@1.2 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EMDomics
Licenses: Expat
Build system: r
Synopsis: Earth Mover's Distance for Differential Analysis of Genomics Data
Description:

The EMDomics algorithm is used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups. Usually the data will be gene expression values from array-based or sequence-based experiments, but data from other types of experiments can also be analyzed (e.g. copy number variation). Traditional methods like Significance Analysis of Microarrays (SAM) and Linear Models for Microarray Data (LIMMA) use significance tests based on summary statistics (mean and standard deviation) of the distributions. This approach lacks power to identify expression differences between groups that show high levels of intra-group heterogeneity. The Earth Mover's Distance (EMD) algorithm instead computes the "work" needed to transform one distribution into another, thus providing a metric of the overall difference in shape between two distributions. Permutation of sample labels is used to generate q-values for the observed EMD scores. This package also incorporates the Komolgorov-Smirnov (K-S) test and the Cramer von Mises test (CVM), which are both common distribution comparison tests.

r-edirquery 1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/EDIRquery
Licenses: GPL 3
Build system: r
Synopsis: Query the EDIR Database For Specific Gene
Description:

EDIRquery provides a tool to search for genes of interest within the Exome Database of Interspersed Repeats (EDIR). A gene name is a required input, and users can additionally specify repeat sequence lengths, minimum and maximum distance between sequences, and whether to allow a 1-bp mismatch. Outputs include a summary of results by repeat length, as well as a dataframe of query results. Example data provided includes a subset of the data for the gene GAA (ENSG00000171298). To query the full database requires providing a path to the downloaded database files as a parameter.

r-ecoliasv2cdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/ecoliasv2cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: ecoliasv2cdf
Description:

This package provides a package containing an environment representing the Ecoli_ASv2.CDF file.

r-eximir 2.52.0
Propagated dependencies: r-preprocesscore@1.72.0 r-limma@3.66.0 r-biobase@2.70.0 r-affyio@1.80.0 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/ExiMiR
Licenses: GPL 2
Build system: r
Synopsis: R functions for the normalization of Exiqon miRNA array data
Description:

This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.

r-epinem 1.34.0
Propagated dependencies: r-rcolorbrewer@1.1-3 r-pcalg@2.7-12 r-mnem@1.26.0 r-minet@3.68.0 r-latticeextra@0.6-31 r-lattice@0.22-7 r-latex2exp@0.9.6 r-igraph@2.2.1 r-gtools@3.9.5 r-graph@1.88.0 r-e1071@1.7-16 r-boutroslab-plotting-general@7.1.5 r-boolnet@2.1.9
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/cbg-ethz/epiNEM/
Licenses: GPL 3
Build system: r
Synopsis: epiNEM
Description:

epiNEM is an extension of the original Nested Effects Models (NEM). EpiNEM is able to take into account double knockouts and infer more complex network signalling pathways. It is tailored towards large scale double knock-out screens.

r-edge 2.42.0
Propagated dependencies: r-sva@3.58.0 r-qvalue@2.42.0 r-mass@7.3-65 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/jdstorey/edge
Licenses: Expat
Build system: r
Synopsis: Extraction of Differential Gene Expression
Description:

The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and generalized likelihood ratio tests (equivalent to F-tests and t-tests) are implemented for general study designs. Special functions are available to facilitate the analysis of common study designs, including time course experiments. Other packages such as sva and qvalue are integrated in edge to provide a wide range of tools for gene expression analysis.

r-epivizrchart 1.32.0
Propagated dependencies: r-rjson@0.2.23 r-htmltools@0.5.8.1 r-epivizrserver@1.38.0 r-epivizrdata@1.38.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/epivizrChart
Licenses: Artistic License 2.0
Build system: r
Synopsis: R interface to epiviz web components
Description:

This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used to generate interactive R markdown/notebook documents or can be visualized in the R Studio's default viewer.

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Total results: 69112