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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-cytomem 1.14.0
Propagated dependencies: r-matrixstats@1.5.0 r-gplots@3.2.0 r-flowcore@2.22.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/cytolab/cytoMEM
Licenses: GPL 3
Build system: r
Synopsis: Marker Enrichment Modeling (MEM)
Description:

MEM, Marker Enrichment Modeling, automatically generates and displays quantitative labels for cell populations that have been identified from single-cell data. The input for MEM is a dataset that has pre-clustered or pre-gated populations with cells in rows and features in columns. Labels convey a list of measured features and the features levels of relative enrichment on each population. MEM can be applied to a wide variety of data types and can compare between MEM labels from flow cytometry, mass cytometry, single cell RNA-seq, and spectral flow cytometry using RMSD.

r-ccplotr 1.8.0
Propagated dependencies: r-viridis@0.6.5 r-tidyr@1.3.1 r-tibble@3.3.0 r-stringr@1.6.0 r-scatterpie@0.2.6 r-scales@1.4.0 r-rcolorbrewer@1.1-3 r-plyr@1.8.9 r-patchwork@1.3.2 r-igraph@2.2.1 r-ggtext@0.1.2 r-ggraph@2.2.2 r-ggplot2@4.0.1 r-ggh4x@0.3.1 r-forcats@1.0.1 r-dplyr@1.1.4 r-complexheatmap@2.26.0 r-circlize@0.4.16
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/Sarah145/CCPlotR
Licenses: Expat
Build system: r
Synopsis: Plots For Visualising Cell-Cell Interactions
Description:

CCPlotR is an R package for visualising results from tools that predict cell-cell interactions from single-cell RNA-seq data. These plots are generic and can be used to visualise results from multiple tools such as Liana, CellPhoneDB, NATMI etc.

r-carnival 2.20.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-stringr@1.6.0 r-rmarkdown@2.30 r-rjson@0.2.23 r-readr@2.1.6 r-lpsolve@5.6.23 r-igraph@2.2.1 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/saezlab/CARNIVAL
Licenses: GPL 3
Build system: r
Synopsis: CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming
Description:

An upgraded causal reasoning tool from Melas et al in R with updated assignments of TFs weights from PROGENy scores. Optimization parameters can be freely adjusted and multiple solutions can be obtained and aggregated.

r-csoa 1.0.0
Propagated dependencies: r-wesanderson@0.3.7 r-textshape@1.7.5 r-summarizedexperiment@1.40.0 r-spatstat-utils@3.2-0 r-sgof@2.3.5 r-seuratobject@5.2.0 r-seurat@5.3.1 r-rlang@1.1.6 r-reshape2@1.4.5 r-qs@0.27.3 r-kerntools@1.2.1 r-henna@0.3.4 r-ggplot2@4.0.1 r-dplyr@1.1.4 r-bayesbio@1.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/andrei-stoica26/CSOA
Licenses: Expat
Build system: r
Synopsis: Calculate per-cell gene signature scores in scRNA-seq data using cell set overlaps
Description:

Cell Set Overlap Analysis (CSOA) is a tool for calculating per-cell gene signature scores in an scRNA-seq dataset. CSOA constructs a set for each gene in the signature, consisting of the cells that highly express the gene. Next, all overlaps of pairs of cell sets are computed, ranked, filtered and scored. The CSOA per-cell score is calculated by summing up all products of the overlap scores and the min-max-normalized expression of the two involved genes. CSOA can run on a Seurat object, a SingleCellExperiment object, a matrix and a dgCMatrix.

r-cnvgsadata 1.46.0
Propagated dependencies: r-cnvgsa@1.54.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cnvGSAdata
Licenses: LGPL 2.0+
Build system: r
Synopsis: Data used in the vignette of the cnvGSA package
Description:

This package contains the data used in the vignette of the cnvGSA package.

r-clariomdhumanprobeset-db 8.8.0
Propagated dependencies: r-org-hs-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/clariomdhumanprobeset.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix clariomdhuman annotation data (chip clariomdhumanprobeset)
Description:

Affymetrix clariomdhuman annotation data (chip clariomdhumanprobeset) assembled using data from public repositories.

r-crisprball 1.6.0
Propagated dependencies: r-shinywidgets@0.9.0 r-shinyjs@2.1.0 r-shinyjqui@0.4.1 r-shinycssloaders@1.1.0 r-shinybs@0.61.1 r-shiny@1.11.1 r-plotly@4.11.0 r-pcatools@2.20.0 r-matrixstats@1.5.0 r-interactivecomplexheatmap@1.18.1 r-htmlwidgets@1.6.4 r-ggplot2@4.0.1 r-dt@0.34.0 r-dittoseq@1.22.0 r-complexheatmap@2.26.0 r-colourpicker@1.3.0 r-circlize@0.4.16
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/j-andrews7/CRISPRball
Licenses: Expat
Build system: r
Synopsis: Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering
Description:

This package provides a Shiny application for visualization, exploration, comparison, and filtering of CRISPR screens analyzed with MAGeCK RRA or MLE. Features include interactive plots with on-click labeling, full customization of plot aesthetics, data upload and/or download, and much more. Quickly and easily explore your CRISPR screen results and generate publication-quality figures in seconds.

r-chipxpress 1.54.0
Propagated dependencies: r-geoquery@2.78.0 r-frma@1.62.0 r-biobase@2.70.0 r-bigmemory@4.6.4 r-biganalytics@1.1.22 r-affy@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/ChIPXpress
Licenses: FSDG-compatible
Build system: r
Synopsis: ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
Description:

ChIPXpress takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.

r-conumee 1.44.0
Propagated dependencies: r-seqinfo@1.0.0 r-rtracklayer@1.70.0 r-minfi@1.56.0 r-iranges@2.44.0 r-illuminahumanmethylationepicmanifest@0.3.0 r-illuminahumanmethylationepicanno-ilm10b2-hg19@0.6.0 r-illuminahumanmethylation450kmanifest@0.4.0 r-illuminahumanmethylation450kanno-ilmn12-hg19@0.6.1 r-genomicranges@1.62.0 r-dnacopy@1.84.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/conumee
Licenses: GPL 2+
Build system: r
Synopsis: Enhanced copy-number variation analysis using Illumina DNA methylation arrays
Description:

This package contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using Illumina 450k or EPIC methylation arrays.

r-cogena 1.44.0
Propagated dependencies: r-tidyr@1.3.1 r-tibble@3.3.0 r-stringr@1.6.0 r-reshape2@1.4.5 r-mclust@6.1.2 r-kohonen@3.0.12 r-gplots@3.2.0 r-ggplot2@4.0.1 r-foreach@1.5.2 r-fastcluster@1.3.0 r-dplyr@1.1.4 r-doparallel@1.0.17 r-devtools@2.4.6 r-corrplot@0.95 r-cluster@2.1.8.1 r-class@7.3-23 r-biwt@1.0.1 r-biobase@2.70.0 r-apcluster@1.4.14 r-amap@0.8-20
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/zhilongjia/cogena
Licenses: LGPL 3
Build system: r
Synopsis: co-expressed gene-set enrichment analysis
Description:

cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.

r-curatedbreastdata 2.38.0
Propagated dependencies: r-xml@3.99-0.20 r-impute@1.84.0 r-ggplot2@4.0.1 r-biocstyle@2.38.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/curatedBreastData
Licenses: GPL 2+
Build system: r
Synopsis: Curated breast cancer gene expression data with survival and treatment information
Description:

Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets.

r-cftools 1.10.0
Propagated dependencies: r-rcpp@1.1.0 r-r-utils@2.13.0 r-genomicranges@1.62.0 r-cftoolsdata@1.8.0 r-bh@1.87.0-1 r-basilisk@1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/jasminezhoulab/cfTools
Licenses: FSDG-compatible
Build system: r
Synopsis: Informatics Tools for Cell-Free DNA Study
Description:

The cfTools R package provides methods for cell-free DNA (cfDNA) methylation data analysis to facilitate cfDNA-based studies. Given the methylation sequencing data of a cfDNA sample, for each cancer marker or tissue marker, we deconvolve the tumor-derived or tissue-specific reads from all reads falling in the marker region. Our read-based deconvolution algorithm exploits the pervasiveness of DNA methylation for signal enhancement, therefore can sensitively identify a trace amount of tumor-specific or tissue-specific cfDNA in plasma. cfTools provides functions for (1) cancer detection: sensitively detect tumor-derived cfDNA and estimate the tumor-derived cfDNA fraction (tumor burden); (2) tissue deconvolution: infer the tissue type composition and the cfDNA fraction of multiple tissue types for a plasma cfDNA sample. These functions can serve as foundations for more advanced cfDNA-based studies, including cancer diagnosis and disease monitoring.

r-coseq 1.34.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-scales@1.4.0 r-s4vectors@0.48.0 r-rmixmod@2.1.10 r-mvtnorm@1.3-3 r-htsfilter@1.50.0 r-htscluster@2.0.11 r-ggplot2@4.0.1 r-edger@4.8.0 r-e1071@1.7-16 r-deseq2@1.50.2 r-corrplot@0.95 r-compositions@2.0-9 r-capushe@1.1.3 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/coseq
Licenses: GPL 3
Build system: r
Synopsis: Co-Expression Analysis of Sequencing Data
Description:

Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.

r-chipenrich-data 2.34.0
Propagated dependencies: r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-readr@2.1.6 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomeinfodb@1.46.0 r-biocgenerics@0.56.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/chipenrich.data
Licenses: GPL 3
Build system: r
Synopsis: Companion package to chipenrich
Description:

Supporting data for the chipenrich package. Includes pre-defined gene sets, gene locus definitions, and mappability estimates.

r-coralysis 1.0.0
Propagated dependencies: r-withr@3.0.2 r-uwot@0.2.4 r-umap@0.2.10.0 r-tidyr@1.3.1 r-summarizedexperiment@1.40.0 r-sparsematrixstats@1.22.0 r-sparsem@1.84-2 r-singlecellexperiment@1.32.0 r-scran@1.38.0 r-scatterpie@0.2.6 r-s4vectors@0.48.0 r-rtsne@0.17 r-rspectra@0.16-2 r-reshape2@1.4.5 r-rcolorbrewer@1.1-3 r-rann@2.6.2 r-pheatmap@1.0.13 r-matrixstats@1.5.0 r-matrix@1.7-4 r-liblinear@2.10-24 r-irlba@2.3.5.1 r-ggrepel@0.9.6 r-ggrastr@1.0.2 r-ggplot2@4.0.1 r-flexclust@1.5.0 r-dplyr@1.1.4 r-cowplot@1.2.0 r-class@7.3-23 r-biocparallel@1.44.0 r-aricode@1.0.3
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/elolab/Coralysis
Licenses: GPL 3
Build system: r
Synopsis: Coralysis sensitive identification of imbalanced cell types and states in single-cell data via multi-level integration
Description:

Coralysis is an R package featuring a multi-level integration algorithm for sensitive integration, reference-mapping, and cell-state identification in single-cell data. The multi-level integration algorithm is inspired by the process of assembling a puzzle - where one begins by grouping pieces based on low-to high-level features, such as color and shading, before looking into shape and patterns. This approach progressively blends the batch effects and separates cell types across multiple rounds of divisive clustering.

r-cadd-v1-6-hg19 3.18.1
Propagated dependencies: r-genomicscores@2.22.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cadd.v1.6.hg19
Licenses: Artistic License 2.0
Build system: r
Synopsis: CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg19
Description:

Store University of Washington CADD v1.6 hg19 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg19 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.

r-compounddb 1.14.2
Propagated dependencies: r-xml2@1.5.0 r-tibble@3.3.0 r-stringi@1.8.7 r-spectra@1.20.0 r-s4vectors@0.48.0 r-rsqlite@2.4.4 r-protgenerics@1.42.0 r-mscoreutils@1.21.0 r-metabocoreutils@1.18.1 r-jsonlite@2.0.0 r-iranges@2.44.0 r-dplyr@1.1.4 r-dbplyr@2.5.1 r-dbi@1.2.3 r-chemminer@3.62.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0 r-biobase@2.70.0 r-annotationfilter@1.34.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/RforMassSpectrometry/CompoundDb
Licenses: Artistic License 2.0
Build system: r
Synopsis: Creating and Using (Chemical) Compound Annotation Databases
Description:

CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.

r-coveb 1.36.0
Propagated dependencies: r-mvtnorm@1.3-3 r-matrix@1.7-4 r-laplacesdemon@16.1.6 r-igraph@2.2.1 r-gsl@2.1-9 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/covEB
Licenses: GPL 3
Build system: r
Synopsis: Empirical Bayes estimate of block diagonal covariance matrices
Description:

Using bayesian methods to estimate correlation matrices assuming that they can be written and estimated as block diagonal matrices. These block diagonal matrices are determined using shrinkage parameters that values below this parameter to zero.

r-cosmic-67 1.46.0
Propagated dependencies: r-variantannotation@1.56.0 r-summarizedexperiment@1.40.0 r-genomicranges@1.62.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/COSMIC.67
Licenses: GPL 3
Build system: r
Synopsis: COSMIC.67
Description:

COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24).

r-customcmpdb 1.20.0
Propagated dependencies: r-xml@3.99-0.20 r-rsqlite@2.4.4 r-rappdirs@0.3.3 r-chemminer@3.62.0 r-biocfilecache@3.0.0 r-annotationhub@4.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/yduan004/customCMPdb/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Customize and Query Compound Annotation Database
Description:

This package serves as a query interface for important community collections of small molecules, while also allowing users to include custom compound collections.

r-cellscape 1.34.0
Propagated dependencies: r-stringr@1.6.0 r-reshape2@1.4.5 r-jsonlite@2.0.0 r-htmlwidgets@1.6.4 r-gtools@3.9.5 r-dplyr@1.1.4
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cellscape
Licenses: GPL 3
Build system: r
Synopsis: Explores single cell copy number profiles in the context of a single cell tree
Description:

CellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of source-target edges to support arbitrary representations, where each node may or may not have associated genomic data. The output of CellScape is an interactive interface displaying a single cell phylogeny and a cell-by-locus genomic heatmap representing the mutation status in each cell for each locus.

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

r-cordon 1.28.0
Propagated dependencies: r-stringr@1.6.0 r-purrr@1.2.0 r-ggplot2@4.0.1 r-dplyr@1.1.4 r-data-table@1.17.8 r-biostrings@2.78.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/BioinfoHR/coRdon
Licenses: Artistic License 2.0
Build system: r
Synopsis: Codon Usage Analysis and Prediction of Gene Expressivity
Description:

Tool for analysis of codon usage in various unannotated or KEGG/COG annotated DNA sequences. Calculates different measures of CU bias and CU-based predictors of gene expressivity, and performs gene set enrichment analysis for annotated sequences. Implements several methods for visualization of CU and enrichment analysis results.

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Total results: 68655