_            _    _        _         _
      /\ \         /\ \ /\ \     /\_\      / /\
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      /\__ \     / /\ \ \\ \ \_/ / /     / / /\ \__
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    / / /\ \ \ / / /  \ \_\\ \ \_/      \ \ \ \/___/
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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-alabaster-sfe 1.2.0
Propagated dependencies: r-xml2@1.5.0 r-terra@1.8-86 r-summarizedexperiment@1.40.0 r-spdep@1.4-1 r-spatialreg@1.4-2 r-spatialfeatureexperiment@1.12.1 r-singlecellexperiment@1.32.0 r-sfarrow@0.4.1 r-s4vectors@0.48.0 r-rbioformats@1.10.0 r-jsonlite@2.0.0 r-ebimage@4.52.0 r-alabaster-spatial@1.10.0 r-alabaster-sce@1.10.0 r-alabaster-base@1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://pachterlab.github.io/alabaster.sfe/
Licenses: Expat
Build system: r
Synopsis: Language agnostic on disk serialization of SpatialFeatureExperiment
Description:

Builds upon the existing ArtifactDB project, expending alabaster.spatial for language agnostic on disk serialization of SpatialFeatureExperiment.

r-adme16cod-db 3.4.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/adme16cod.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod)
Description:

Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod) assembled using data from public repositories.

r-alabaster 1.10.0
Propagated dependencies: r-alabaster-vcf@1.10.0 r-alabaster-string@1.10.0 r-alabaster-spatial@1.10.0 r-alabaster-se@1.10.0 r-alabaster-sce@1.10.0 r-alabaster-ranges@1.10.0 r-alabaster-matrix@1.10.0 r-alabaster-mae@1.10.0 r-alabaster-bumpy@1.10.0 r-alabaster-base@1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/alabaster
Licenses: Expat
Build system: r
Synopsis: Umbrella for the Alabaster Framework
Description:

Umbrella for the alabaster suite, providing a single-line import for all alabaster.* packages. Installing this package ensures that all known alabaster.* packages are also installed, avoiding problems with missing packages when a staging method or loading function is dynamically requested. Obviously, this comes at the cost of needing to install more packages, so advanced users and application developers may prefer to install the required alabaster.* packages individually.

r-alphamissense-v2023-hg19 3.18.2
Propagated dependencies: r-genomicscores@2.22.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/AlphaMissense.v2023.hg19
Licenses: Artistic License 2.0
Build system: r
Synopsis: AlphaMissense v2023 Pathogenicity Scores AnnotationHub Resource Metadata for hg19
Description:

Store Google DeepMind AlphaMissense v2023 hg19 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for Google DeepMind AlphaMissense v2023 hg19 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.

r-adverscarial 1.8.0
Propagated dependencies: r-s4vectors@0.48.0 r-gtools@3.9.5 r-delayedarray@0.36.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/adverSCarial
Licenses: Expat
Build system: r
Synopsis: adverSCarial, generate and analyze the vulnerability of scRNA-seq classifier to adversarial attacks
Description:

adverSCarial is an R Package designed for generating and analyzing the vulnerability of scRNA-seq classifiers to adversarial attacks. The package is versatile and provides a format for integrating any type of classifier. It offers functions for studying and generating two types of attacks, single gene attack and max change attack. The single-gene attack involves making a small modification to the input to alter the classification. The max-change attack involves making a large modification to the input without changing its classification. The CGD attack is based on an estimated gradient descent. against adversarial attacks. The package provides a comprehensive solution for evaluating the robustness of scRNA-seq classifiers against adversarial attacks.

r-alabaster-bumpy 1.10.0
Propagated dependencies: r-s4vectors@0.48.0 r-rhdf5@2.54.0 r-matrix@1.7-4 r-iranges@2.44.0 r-bumpymatrix@1.18.0 r-biocgenerics@0.56.0 r-alabaster-base@1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/alabaster.bumpy
Licenses: Expat
Build system: r
Synopsis: Save and Load BumpyMatrices to/from file
Description:

Save BumpyMatrix objects into file artifacts, and load them back into memory. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

r-anansi 1.0.0
Propagated dependencies: r-treesummarizedexperiment@2.18.0 r-tidygraph@1.3.1 r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-s7@0.2.1 r-s4vectors@0.48.0 r-rlang@1.1.6 r-patchwork@1.3.2 r-multiassayexperiment@1.36.1 r-matrix@1.7-4 r-igraph@2.2.1 r-ggraph@2.2.2 r-ggplot2@4.0.1 r-ggforce@0.5.0 r-forcats@1.0.1
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://github.com/thomazbastiaanssen/anansi
Licenses: GPL 3
Build system: r
Synopsis: Annotation-Based Analysis of Specific Interactions
Description:

Studies including both microbiome and metabolomics data are becoming more common. Often, it would be helpful to integrate both datasets in order to see if they corroborate each others patterns. All vs all association is imprecise and likely to yield spurious associations. This package takes a knowledge-based approach to constrain association search space, only considering metabolite-function pairs that have been recorded in a pathway database. This package also provides a framework to assess differential association.

r-ath1121501probe 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/ath1121501probe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type ath1121501
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 ATH1-121501\_probe\_tab.

r-atacseqtfea 1.12.0
Propagated dependencies: r-tfbstools@1.48.0 r-summarizedexperiment@1.40.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rsamtools@2.26.0 r-pracma@2.4.6 r-motifmatchr@1.32.0 r-matrix@1.7-4 r-limma@3.66.0 r-iranges@2.44.0 r-ggrepel@0.9.6 r-ggplot2@4.0.1 r-genomicranges@1.62.0 r-genomicalignments@1.46.0 r-dplyr@1.1.4 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://github.com/jianhong/ATACseqTFEA
Licenses: GPL 3
Build system: r
Synopsis: Transcription Factor Enrichment Analysis for ATAC-seq
Description:

Assay for Transpose-Accessible Chromatin using sequencing (ATAC-seq) is a technique to assess genome-wide chromatin accessibility by probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome. ATACseqTFEA is an improvement of the current computational method that detects differential activity of transcription factors (TFs). ATACseqTFEA not only uses the difference of open region information, but also (or emphasizes) the difference of TFs footprints (cutting sites or insertion sites). ATACseqTFEA provides an easy, rigorous way to broadly assess TF activity changes between two conditions.

r-alabaster-vcf 1.10.0
Propagated dependencies: r-variantannotation@1.56.0 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-alabaster-string@1.10.0 r-alabaster-se@1.10.0 r-alabaster-base@1.10.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/alabaster.vcf
Licenses: Expat
Build system: r
Synopsis: Save and Load Variant Data to/from File
Description:

Save variant calling SummarizedExperiment to file and load them back as VCF objects. This is a more portable alternative to serialization of such objects into RDS files. Each artifact is associated with metadata for further interpretation; downstream applications can enrich this metadata with context-specific properties.

r-ahmassbank 1.10.0
Propagated dependencies: r-annotationhubdata@1.40.0
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://github.com/jorainer/AHMassBank
Licenses: Artistic License 2.0
Build system: r
Synopsis: MassBank Annotation Resources for AnnotationHub
Description:

Supplies AnnotationHub with MassBank metabolite/compound annotations bundled in CompDb SQLite databases. CompDb SQLite databases contain general compound annotation as well as fragment spectra representing fragmentation patterns of compounds ions. MassBank data is retrieved from https://massbank.eu/MassBank and processed using helper functions from the CompoundDb Bioconductor package into redistributable SQLite databases.

r-adapt 1.4.0
Propagated dependencies: r-rcppparallel@5.1.11-1 r-rcpparmadillo@15.2.2-1 r-rcpp@1.1.0 r-phyloseq@1.54.0 r-ggrepel@0.9.6 r-ggplot2@4.0.1
Channel: guix-bioc
Location: guix-bioc/packages/a.scm (guix-bioc packages a)
Home page: https://bioconductor.org/packages/ADAPT
Licenses: Expat
Build system: r
Synopsis: Analysis of Microbiome Differential Abundance by Pooling Tobit Models
Description:

ADAPT carries out differential abundance analysis for microbiome metagenomics data in phyloseq format. It has two innovations. One is to treat zero counts as left censored and use Tobit models for log count ratios. The other is an innovative way to find non-differentially abundant taxa as reference, then use the reference taxa to find the differentially abundant ones.

r-brgedata 1.32.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/brgedata
Licenses: Expat
Build system: r
Synopsis: Exposures, Gene Expression and Methylation data for ilustration purpouses
Description:

This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome.

r-bindingsitefinder 2.8.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-rlang@1.1.6 r-rcolorbrewer@1.1-3 r-plyr@1.8.9 r-matrixstats@1.5.0 r-lifecycle@1.0.4 r-kableextra@1.4.0 r-iranges@2.44.0 r-ggplot2@4.0.1 r-ggforce@0.5.0 r-ggdist@3.3.3 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-genomeinfodb@1.46.0 r-forcats@1.0.1 r-dplyr@1.1.4 r-complexheatmap@2.26.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BindingSiteFinder
Licenses: Artistic License 2.0
Build system: r
Synopsis: Binding site defintion based on iCLIP data
Description:

Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.

r-bsgenome-btaurus-ucsc-bostau3-masked 1.3.99
Propagated dependencies: r-bsgenome-btaurus-ucsc-bostau3@1.4.0 r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Btaurus.UCSC.bosTau3.masked
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full masked genome sequences for Bos taurus (UCSC version bosTau3)
Description:

Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

r-bsgenome-ptroglodytes-ucsc-pantro2-masked 1.3.99
Propagated dependencies: r-bsgenome-ptroglodytes-ucsc-pantro2@1.4.0 r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Ptroglodytes.UCSC.panTro2.masked
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full masked genome sequences for Pan troglodytes (UCSC version panTro2)
Description:

Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro2, Mar. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ptroglodytes.UCSC.panTro2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.

r-beadarrayusecases 1.47.0
Propagated dependencies: r-limma@3.66.0 r-geoquery@2.78.0 r-beadarray@2.58.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BeadArrayUseCases
Licenses: GPL 2
Build system: r
Synopsis: Analysing Illumina BeadArray expression data using Bioconductor
Description:

Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor.

r-bsgenome-scerevisiae-ucsc-saccer1 1.4.0
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Scerevisiae.UCSC.sacCer1
Licenses: Artistic License 2.0
Build system: r
Synopsis: Saccharomyces cerevisiae (Yeast) full genome (UCSC version sacCer1)
Description:

Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer1, Oct. 2003) and stored in Biostrings objects.

r-breastcancertransbig 1.48.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: http://compbio.dfci.harvard.edu/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Gene expression dataset published by Desmedt et al. [2007] (TRANSBIG)
Description:

Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet.

r-bsgenome-amellifera-ucsc-apimel2-masked 1.3.99
Propagated dependencies: r-bsgenome-amellifera-ucsc-apimel2@1.4.0 r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Amellifera.UCSC.apiMel2.masked
Licenses: Artistic License 2.0
Build system: r
Synopsis: Full masked genome sequences for Apis mellifera (UCSC version apiMel2)
Description:

Full genome sequences for Apis mellifera (Honey Bee) as provided by UCSC (apiMel2, Jan. 2005) and stored in Biostrings objects. The sequences are the same as in BSgenome.Amellifera.UCSC.apiMel2, except that each of them has the 3 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), and (3) the mask of repeats from RepeatMasker (RM mask). Only the AGAPS and AMB masks are "active" by default.

r-biodbchebi 1.16.0
Propagated dependencies: r-r6@2.6.1 r-biodb@1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://github.com/pkrog/biodbChebi
Licenses: AGPL 3
Build system: r
Synopsis: biodbChebi, a library for connecting to the ChEBI Database
Description:

The biodbChebi library provides access to the ChEBI Database, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name, mass or other fields.

r-biochail 1.10.0
Propagated dependencies: r-reticulate@1.44.1 r-dplyr@1.1.4 r-biocgenerics@0.56.0 r-biocfilecache@3.0.0 r-basilisk@1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://github.com/vjcitn/BiocHail
Licenses: Artistic License 2.0
Build system: r
Synopsis: basilisk and hail
Description:

Use hail via basilisk when appropriate, or via reticulate. This package can be used in terra.bio to interact with UK Biobank resources processed by hail.is.

r-bsgenome-hsapiens-ucsc-hg38-dbsnp151-minor 0.0.9999
Propagated dependencies: r-bsgenome@1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38.dbSNP151.minor
Licenses: FSDG-compatible
Build system: r
Synopsis: Full genome sequences for Homo sapiens (UCSC version hg38, based on GRCh38.p12) with injected minor alleles (dbSNP151)
Description:

Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with minor alleles injected from dbSNP151, and stored in Biostrings objects. Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, based on GRCh38.p12) with minor alleles injected from dbSNP151, and stored in Biostrings objects. Only common single nucleotide variants (SNVs) with at least one alternate allele with frequency greater than 0.01 were considered. For SNVs with more than 1 alternate allele, the most frequent allele was chosen as the minor allele to be injected into the reference genome.

r-biocfhir 1.12.0
Propagated dependencies: r-visnetwork@2.1.4 r-tidyr@1.3.1 r-shiny@1.11.1 r-jsonlite@2.0.0 r-graph@1.88.0 r-dt@0.34.0 r-dplyr@1.1.4 r-biocbaseutils@1.12.0
Channel: guix-bioc
Location: guix-bioc/packages/b.scm (guix-bioc packages b)
Home page: https://github.com/vjcitn/BiocFHIR
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illustration of FHIR ingestion and transformation using R
Description:

FHIR R4 bundles in JSON format are derived from https://synthea.mitre.org/downloads. Transformation inspired by a kaggle notebook published by Dr Alexander Scarlat, https://www.kaggle.com/code/drscarlat/fhir-starter-parse-healthcare-bundles-into-tables. This is a very limited illustration of some basic parsing and reorganization processes. Additional tooling will be required to move beyond the Synthea data illustrations.

Total results: 2909