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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-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-emtdata 1.18.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-experimenthub@3.0.0 r-edger@4.8.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/DavisLaboratory/emtdata
Licenses: GPL 3
Build system: r
Synopsis: An ExperimentHub Package for data sets with an Epithelial to Mesenchymal Transition (EMT)
Description:

This package provides pre-processed RNA-seq data where the epithelial to mesenchymal transition was induced on cell lines. These data come from three publications Cursons et al. (2015), Cursons etl al. (2018) and Foroutan et al. (2017). In each of these publications, EMT was induces across multiple cell lines following treatment by TGFb among other stimulants. This data will be useful in determining the regulatory programs modified in order to achieve an EMT. Data were processed by the Davis laboratory in the Bioinformatics division at WEHI.

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-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.

r-eds 1.12.0
Dependencies: zlib@1.3.1
Propagated dependencies: r-rcpp@1.1.0 r-matrix@1.7-4
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/mikelove/eds
Licenses: GPL 2
Build system: r
Synopsis: eds: Low-level reader for Alevin EDS format
Description:

This packages provides a single function, readEDS. This is a low-level utility for reading in Alevin EDS format into R. This function is not designed for end-users but instead the package is predominantly for simplifying package dependency graph for other Bioconductor packages.

r-ecoliprobe 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/ecoliprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type ecoli
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 E\_coli\_probe\_tab.

r-epistasisga 1.12.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/mnodzenski/epistasisGA
Licenses: GPL 3
Build system: r
Synopsis: An R package to identify multi-snp effects in nuclear family studies using the GADGETS method
Description:

This package runs the GADGETS method to identify epistatic effects in nuclear family studies. It also provides functions for permutation-based inference and graphical visualization of the results.

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-epivizrdata 1.38.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-organismdbi@1.52.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-epivizrserver@1.38.0 r-ensembldb@2.34.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: http://epiviz.github.io
Licenses: Expat
Build system: r
Synopsis: Data Management API for epiviz interactive visualization app
Description:

Serve data from Bioconductor Objects through a WebSocket connection.

r-evaluomer 1.26.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/neobernad/evaluomeR
Licenses: GPL 3
Build system: r
Synopsis: Evaluation of Bioinformatics Metrics
Description:

Evaluating the reliability of your own metrics and the measurements done on your own datasets by analysing the stability and goodness of the classifications of such metrics.

r-ewce 1.18.1
Propagated dependencies: r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-singlecellexperiment@1.32.0 r-rnomni@1.0.1.2 r-reshape2@1.4.5 r-orthogene@1.16.1 r-matrix@1.7-4 r-limma@3.66.0 r-hgnchelper@0.8.15 r-ggplot2@4.0.1 r-ewcedata@1.18.0 r-dplyr@1.1.4 r-delayedarray@0.36.0 r-data-table@1.17.8 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/NathanSkene/EWCE
Licenses: GPL 3
Build system: r
Synopsis: Expression Weighted Celltype Enrichment
Description:

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-esatac 1.32.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://github.com/wzthu/esATAC
Licenses: GPL 3 FSDG-compatible
Build system: r
Synopsis: An Easy-to-use Systematic pipeline for ATACseq data analysis
Description:

This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.

r-easyreporting 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/e.scm (guix-bioc packages e)
Home page: https://bioconductor.org/packages/easyreporting
Licenses: Artistic License 2.0
Build system: r
Synopsis: Helps creating report for improving Reproducible Computational Research
Description:

An S4 class for facilitating the automated creation of rmarkdown files inside other packages/software even without knowing rmarkdown language. Best if implemented in functions as "recursive" style programming.

r-fieldeffectcrc 1.20.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: http://bioconductor.org/packages/release/bioc/html/FieldEffectCrc.html
Licenses: Artistic License 2.0
Build system: r
Synopsis: Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as SummarizedExperiment objects
Description:

Processed RNA-seq data for 1,139 human primary colorectal tissue samples across three phenotypes, including tumor, normal adjacent-to-tumor, and healthy, available as Synapse ID syn22237139 on synapse.org. Data have been parsed into SummarizedExperiment objects available via ExperimentHub to facilitate reproducibility and extension of results from Dampier et al. (PMCID: PMC7386360, PMID: 32764205).

r-fedup 1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/rosscm/fedup
Licenses: Expat
Build system: r
Synopsis: Fisher's Test for Enrichment and Depletion of User-Defined Pathways
Description:

An R package that tests for enrichment and depletion of user-defined pathways using a Fisher's exact test. The method is designed for versatile pathway annotation formats (eg. gmt, txt, xlsx) to allow the user to run pathway analysis on custom annotations. This package is also integrated with Cytoscape to provide network-based pathway visualization that enhances the interpretability of the results.

r-flowcybar 1.46.0
Propagated dependencies: r-vegan@2.7-2 r-gplots@3.2.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: http://www.ufz.de/index.php?de=16773
Licenses: GPL 2
Build system: r
Synopsis: Analyze flow cytometric data using gate information
Description:

This package provides a package to analyze flow cytometric data using gate information to follow population/community dynamics.

r-fdb-ucsc-snp135common-hg19 1.0.0
Propagated dependencies: r-genomicfeatures@1.62.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/FDb.UCSC.snp135common.hg19
Licenses: Artistic License 2.0
Build system: r
Synopsis: UCSC common SNPs track for dbSNP build 135
Description:

makeFeatureDbFromUCSC cannot cope with this track, hence a package.

r-fdb-ucsc-trnas 1.0.1
Propagated dependencies: r-genomicfeatures@1.62.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/FDb.UCSC.tRNAs
Licenses: Artistic License 2.0
Build system: r
Synopsis: Annotation package for FeatureDb object(s)
Description:

Exposes an annotation databases generated from UCSC by exposing these as FeatureDb objects.

r-flowbeads 1.48.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/flowBeads
Licenses: Artistic License 2.0
Build system: r
Synopsis: flowBeads: Analysis of flow bead data
Description:

This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation.

r-flowgraph 1.18.0
Propagated dependencies: r-visnetwork@2.1.4 r-stringr@1.6.0 r-stringi@1.8.7 r-rdpack@2.6.4 r-purrr@1.2.0 r-matrixstats@1.5.0 r-matrix@1.7-4 r-igraph@2.2.1 r-htmlwidgets@1.6.4 r-gridextra@2.3 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-ggiraph@0.9.2 r-future@1.68.0 r-furrr@0.3.1 r-effsize@0.8.1 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/aya49/flowGraph
Licenses: Artistic License 2.0
Build system: r
Synopsis: Identifying differential cell populations in flow cytometry data accounting for marker frequency
Description:

Identifies maximal differential cell populations in flow cytometry data taking into account dependencies between cell populations; flowGraph calculates and plots SpecEnr abundance scores given cell population cell counts.

r-fantom3and4cage 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/FANTOM3and4CAGE
Licenses: GPL 3
Build system: r
Synopsis: CAGE data from FANTOM3 and FANTOM4 projects
Description:

CAGE (Cap Analysis Gene Expression) data from FANTOM3 and FANTOM4 projects produced by RIKEN Omics Science Center.

r-fabiadata 1.48.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: http://www.bioinf.jku.at/software/fabia/fabia.html
Licenses: LGPL 2.1+
Build system: r
Synopsis: Data sets for FABIA (Factor Analysis for Bicluster Acquisition)
Description:

Supplying gene expression data sets for the demos of the biclustering method "Factor Analysis for Bicluster Acquisition" (FABIA). The following three data sets are provided: A) breast cancer (van't Veer, Nature, 2002), B) multiple tissues (Su, PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N Engl J Med, 2002).

r-flowcut 1.20.0
Propagated dependencies: r-flowdensity@1.44.0 r-flowcore@2.22.0 r-e1071@1.7-16 r-cairo@1.7-0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://bioconductor.org/packages/flowCut
Licenses: Artistic License 2.0
Build system: r
Synopsis: Automated Removal of Outlier Events and Flagging of Files Based on Time Versus Fluorescence Analysis
Description:

Common techinical complications such as clogging can result in spurious events and fluorescence intensity shifting, flowCut is designed to detect and remove technical artifacts from your data by removing segments that show statistical differences from other segments.

r-fgga 1.18.0
Propagated dependencies: r-rbgl@1.86.0 r-jsonlite@2.0.0 r-igraph@2.2.1 r-grbase@2.0.3 r-graph@1.88.0 r-e1071@1.7-16 r-curl@7.0.0 r-biocfilecache@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/f.scm (guix-bioc packages f)
Home page: https://github.com/fspetale/fgga
Licenses: GPL 3
Build system: r
Synopsis: Hierarchical ensemble method based on factor graph
Description:

Package that implements the FGGA algorithm. This package provides a hierarchical ensemble method based ob factor graphs for the consistent cross-ontology annotation of protein coding genes. FGGA embodies elements of predicate logic, communication theory, supervised learning and inference in graphical models.

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Total results: 69264