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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-countsimqc 1.28.1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/csoneson/countsimQC
Licenses: FSDG-compatible
Build system: r
Synopsis: Compare Characteristic Features of Count Data Sets
Description:

countsimQC provides functionality to create a comprehensive report comparing a broad range of characteristics across a collection of count matrices. One important use case is the comparison of one or more synthetic count matrices to a real count matrix, possibly the one underlying the simulations. However, any collection of count matrices can be compared.

r-cfassay 1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CFAssay
Licenses: LGPL 2.0+
Build system: r
Synopsis: Statistical analysis for the Colony Formation Assay
Description:

The package provides functions for calculation of linear-quadratic cell survival curves and for ANOVA of experimental 2-way designs along with the colony formation assay.

r-cllmethylation 1.30.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CLLmethylation
Licenses: LGPL 2.0+
Build system: r
Synopsis: Methylation data of primary CLL samples in PACE project
Description:

The package includes DNA methylation data for the primary Chronic Lymphocytic Leukemia samples included in the Primary Blood Cancer Encyclopedia (PACE) project. Raw data from the 450k DNA methylation arrays is stored in the European Genome-Phenome Archive (EGA) under accession number EGAS0000100174. For more information concerning the project please refer to the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) and R/Bioconductor package BloodCancerMultiOmics2017.

r-clumsid 1.26.0
Propagated dependencies: r-sna@2.8 r-s4vectors@0.48.0 r-rcolorbrewer@1.1-3 r-plotly@4.11.0 r-network@1.19.0 r-mzr@2.44.0 r-msnbase@2.36.0 r-gplots@3.2.0 r-ggplot2@4.0.1 r-ggally@2.4.0 r-dbscan@1.2.3 r-biobase@2.70.0 r-ape@5.8-1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/tdepke/CluMSID
Licenses: Expat
Build system: r
Synopsis: Clustering of MS2 Spectra for Metabolite Identification
Description:

CluMSID is a tool that aids the identification of features in untargeted LC-MS/MS analysis by the use of MS2 spectra similarity and unsupervised statistical methods. It offers functions for a complete and customisable workflow from raw data to visualisations and is interfaceable with the xmcs family of preprocessing packages.

r-crupr 1.2.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/akbariomgba/crupR
Licenses: GPL 3
Build system: r
Synopsis: An R package to predict condition-specific enhancers from ChIP-seq data
Description:

An R package that offers a workflow to predict condition-specific enhancers from ChIP-seq data. The prediction of regulatory units is done in four main steps: Step 1 - the normalization of the ChIP-seq counts. Step 2 - the prediction of active enhancers binwise on the whole genome. Step 3 - the condition-specific clustering of the putative active enhancers. Step 4 - the detection of possible target genes of the condition-specific clusters using RNA-seq counts.

r-cmap2data 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cMap2data
Licenses: GPL 3
Build system: r
Synopsis: Connectivity Map (version 2) Data
Description:

Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package.

r-consensusseeker 1.38.0
Propagated dependencies: r-stringr@1.6.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rtracklayer@1.70.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-biocparallel@1.44.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/adeschen/consensusSeekeR
Licenses: Artistic License 2.0
Build system: r
Synopsis: Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Description:

This package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region. In genomic analysis where feature identification generates a position value surrounded by a genomic range, such as ChIP-Seq peaks and nucleosome positions, the replication of an experiment may result in slight differences between predicted values. This package enables the conciliation of the results into consensus regions.

r-clustifyr 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/rnabioco/clustifyr
Licenses: Expat
Build system: r
Synopsis: Classifier for Single-cell RNA-seq Using Cell Clusters
Description:

Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided to assist cell type assignment.

r-cbn2path 1.0.0
Dependencies: gsl@2.8
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/rockwillck/CBN2Path
Licenses: Expat
Build system: r
Synopsis: "CBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjunctive Bayesian Networks
Description:

CBN2Path package provides a unifying interface to facilitate CBN-based quantification, analysis and visualization of cancer progression pathways.

r-cellxgenedp 1.14.0
Propagated dependencies: r-shiny@1.11.1 r-rjsoncons@1.3.2 r-httr@1.4.7 r-dt@0.34.0 r-dplyr@1.1.4 r-curl@7.0.0 r-cli@3.6.5
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://mtmorgan.github.io/cellxgenedp/
Licenses: Artistic License 2.0
Build system: r
Synopsis: Discover and Access Single Cell Data Sets in the CELLxGENE Data Portal
Description:

The cellxgene data portal (https://cellxgene.cziscience.com/) provides a graphical user interface to collections of single-cell sequence data processed in standard ways to count matrix summaries. The cellxgenedp package provides an alternative, R-based inteface, allowind data discovery, viewing, and downloading.

r-canine-db0 3.22.0
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/canine.db0
Licenses: Artistic License 2.0
Build system: r
Synopsis: Base Level Annotation databases for canine
Description:

Base annotation databases for canine, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.

r-cadd-v1-6-hg38 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.hg38
Licenses: Artistic License 2.0
Build system: r
Synopsis: CADD v1.6 Pathogenicity Scores AnnotationHub Resource Metadata for hg38
Description:

Store University of Washington CADD v1.6 hg38 pathogenicity scores AnnotationHub Resource Metadata. Provide provenance and citation information for University of Washington CADD v1.6 hg38 pathogenicity score AnnotationHub resources. Illustrate in a vignette how to access those resources.

r-cytodx 1.30.0
Propagated dependencies: r-rpart-plot@3.1.4 r-rpart@4.1.24 r-glmnet@4.1-10 r-flowcore@2.22.0 r-dplyr@1.1.4 r-doparallel@1.0.17
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CytoDx
Licenses: GPL 2
Build system: r
Synopsis: Robust prediction of clinical outcomes using cytometry data without cell gating
Description:

This package provides functions that predict clinical outcomes using single cell data (such as flow cytometry data, RNA single cell sequencing data) without the requirement of cell gating or clustering.

r-cogito 1.16.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/Cogito
Licenses: LGPL 3
Build system: r
Synopsis: Compare genomic intervals tool - Automated, complete, reproducible and clear report about genomic and epigenomic data sets
Description:

Biological studies often consist of multiple conditions which are examined with different laboratory set ups like RNA-sequencing or ChIP-sequencing. To get an overview about the whole resulting data set, Cogito provides an automated, complete, reproducible and clear report about all samples and basic comparisons between all different samples. This report can be used as documentation about the data set or as starting point for further custom analysis.

r-ctcf 0.99.13
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/dozmorovlab/CTCF
Licenses: Expat
Build system: r
Synopsis: Genomic coordinates of CTCF binding sites, with orientation
Description:

Genomic coordinates of CTCF binding sites, with strand orientation (directionality of binding). Position weight matrices (PWMs) from JASPAR, HOCOMOCO, CIS-BP, CTCFBSDB, SwissRegulon, Jolma 2013, were used to uniformly predict CTCF binding sites using FIMO (default settings) on human (hg18, hg19, hg38, T2T) and mouse (mm9, mm10, mm39) genome assemblies. Extra columns include motif/PWM name (e.g., MA0139.1), score, p-value, q-value, and the motif sequence. It is recommended to filter FIMO-predicted sites by 1e-6 p-value threshold instead of using the default 1e-4 threshold. Experimentally obtained CTCF-bound cis-regulatory elements from ENCODE SCREEN and predicted CTCF sites from CTCFBSDB are also included. Selected data are lifted over from a different genome assembly as we demonstrated liftOver is a viable option to obtain CTCF coordinates in different genome assemblies. CTCF sites obtained using JASPAR's MA0139.1 PWM and filtered at 1e-6 p-value threshold are recommended.

r-cqn 1.56.0
Propagated dependencies: r-quantreg@6.1 r-nor1mix@1.3-3 r-mclust@6.1.2
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/cqn
Licenses: Artistic License 2.0
Build system: r
Synopsis: Conditional quantile normalization
Description:

This package provides a normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.

r-cytomds 1.6.1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://uclouvain-cbio.github.io/CytoMDS
Licenses: GPL 3
Build system: r
Synopsis: Low Dimensions projection of cytometry samples
Description:

This package implements a low dimensional visualization of a set of cytometry samples, in order to visually assess the distances between them. This, in turn, can greatly help the user to identify quality issues like batch effects or outlier samples, and/or check the presence of potential sample clusters that might align with the exeprimental design. The CytoMDS algorithm combines, on the one hand, the concept of Earth Mover's Distance (EMD), a.k.a. Wasserstein metric and, on the other hand, the Multi Dimensional Scaling (MDS) algorithm for the low dimensional projection. Also, the package provides some diagnostic tools for both checking the quality of the MDS projection, as well as tools to help with the interpretation of the axes of the projection.

r-celda 1.26.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/celda
Licenses: Expat
Build system: r
Synopsis: CEllular Latent Dirichlet Allocation
Description:

Celda is a suite of Bayesian hierarchical models for clustering single-cell RNA-sequencing (scRNA-seq) data. It is able to perform "bi-clustering" and simultaneously cluster genes into gene modules and cells into cell subpopulations. It also contains DecontX, a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. A variety of scRNA-seq data visualization functions is also included.

r-curatedmetagenomicdata 3.18.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/waldronlab/curatedMetagenomicData
Licenses: Artistic License 2.0
Build system: r
Synopsis: Curated Metagenomic Data of the Human Microbiome
Description:

The curatedMetagenomicData package provides standardized, curated human microbiome data for novel analyses. It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. The bacterial, fungal, and archaeal taxonomic abundances for each sample were calculated with MetaPhlAn3, and metabolic functional potential was calculated with HUMAnN3. The manually curated sample metadata and standardized metagenomic data are available as (Tree)SummarizedExperiment objects.

r-ccpromise 1.36.0
Propagated dependencies: r-promise@1.62.0 r-gseabase@1.72.0 r-ccp@1.2 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CCPROMISE
Licenses: GPL 2+
Build system: r
Synopsis: PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data
Description:

Perform Canonical correlation between two forms of high demensional genetic data, and associate the first compoent of each form of data with a specific biologically interesting pattern of associations with multiple endpoints. A probe level analysis is also implemented.

r-cosiadata 1.10.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/CoSIAdata
Licenses: Expat
Build system: r
Synopsis: VST normalized RNA-Sequencing data with annotations for multiple species samples from Bgee
Description:

Variance Stabilized Transformation of Read Counts derived from Bgee RNA-Seq Expression Data. Expression Data includes annotations and is across 6 species (Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Drosophila melanogaster, and Caenorhabditis elegans) and across more than 132 tissues. The data is represented as a RData files and is available in ExperimentHub.

r-cepo 1.16.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/Cepo
Licenses: Expat
Build system: r
Synopsis: Cepo for the identification of differentially stable genes
Description:

Defining the identity of a cell is fundamental to understand the heterogeneity of cells to various environmental signals and perturbations. We present Cepo, a new method to explore cell identities from single-cell RNA-sequencing data using differential stability as a new metric to define cell identity genes. Cepo computes cell-type specific gene statistics pertaining to differential stable gene expression.

r-ctsv 1.12.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-spatialexperiment@1.20.0 r-qvalue@2.42.0 r-pscl@1.5.9 r-knitr@1.50 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/jingeyu/CTSV
Licenses: GPL 3
Build system: r
Synopsis: Identification of cell-type-specific spatially variable genes accounting for excess zeros
Description:

The R package CTSV implements the CTSV approach developed by Jinge Yu and Xiangyu Luo that detects cell-type-specific spatially variable genes accounting for excess zeros. CTSV directly models sparse raw count data through a zero-inflated negative binomial regression model, incorporates cell-type proportions, and performs hypothesis testing based on R package pscl. The package outputs p-values and q-values for genes in each cell type, and CTSV is scalable to datasets with tens of thousands of genes measured on hundreds of spots. CTSV can be installed in Windows, Linux, and Mac OS.

r-clariomsmousetranscriptcluster-db 8.8.0
Propagated dependencies: r-org-mm-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/clariomsmousetranscriptcluster.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix clariomsmouse annotation data (chip clariomsmousetranscriptcluster)
Description:

Affymetrix clariomsmouse annotation data (chip clariomsmousetranscriptcluster) assembled using data from public repositories.

Total results: 2911