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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-censcyt 1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/retogerber/censcyt
Licenses: Expat
Build system: r
Synopsis: Differential abundance analysis with a right censored covariate in high-dimensional cytometry
Description:

This package provides methods for differential abundance analysis in high-dimensional cytometry data when a covariate is subject to right censoring (e.g. survival time) based on multiple imputation and generalized linear mixed models.

r-cancer 1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/canceR
Licenses: GPL 2
Build system: r
Synopsis: Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC
Description:

The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

r-ctsge 1.36.0
Propagated dependencies: r-stringr@1.6.0 r-shiny@1.11.1 r-reshape2@1.4.5 r-limma@3.66.0 r-ggplot2@4.0.1 r-ccapp@0.3.5
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/michalsharabi/ctsGE
Licenses: GPL 2
Build system: r
Synopsis: Clustering of Time Series Gene Expression data
Description:

Methodology for supervised clustering of potentially many predictor variables, such as genes etc., in time series datasets Provides functions that help the user assigning genes to predefined set of model profiles.

r-chickencdf 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/chickencdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: chickencdf
Description:

This package provides a package containing an environment representing the Chicken.cdf file.

r-chromheatmap 1.64.0
Propagated dependencies: r-rtracklayer@1.70.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-biocgenerics@0.56.0 r-biobase@2.70.0 r-annotationdbi@1.72.0 r-annotate@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/ChromHeatMap
Licenses: Artistic License 2.0
Build system: r
Synopsis: Heat map plotting by genome coordinate
Description:

The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest.

r-chipsim 1.64.0
Propagated dependencies: r-xvector@0.50.0 r-shortread@1.68.0 r-iranges@2.44.0 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://bioconductor.org/packages/ChIPsim
Licenses: GPL 2+
Build system: r
Synopsis: Simulation of ChIP-seq experiments
Description:

This package provides a general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.

r-codelink 1.78.0
Propagated dependencies: r-limma@3.66.0 r-biocgenerics@0.56.0 r-biobase@2.70.0 r-annotate@1.88.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/ddiez/codelink
Licenses: GPL 2
Build system: r
Synopsis: Manipulation of Codelink microarray data
Description:

This package facilitates reading, preprocessing and manipulating Codelink microarray data. The raw data must be exported as text file using the Codelink software.

r-ctdata 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/CTdata
Licenses: Artistic License 2.0
Build system: r
Synopsis: Data companion to CTexploreR
Description:

Data from publicly available databases (GTEx, CCLE, TCGA and ENCODE) that go with CTexploreR in order to re-define a comprehensive and thoroughly curated list of CT genes and their main characteristics.

r-cycle 1.64.0
Propagated dependencies: r-mfuzz@2.70.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: http://cycle.sysbiolab.eu
Licenses: GPL 2
Build system: r
Synopsis: Significance of periodic expression pattern in time-series data
Description:

Package for assessing the statistical significance of periodic expression based on Fourier analysis and comparison with data generated by different background models.

r-centreannotation 0.99.1
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/slrvv/CENTREannotation
Licenses: Artistic License 2.0
Build system: r
Synopsis: Hub package for the annotation data of CENTRE (GENCODE v40 and SCREEN v3)
Description:

This is an AnnotationHub package for the CENTRE Bioconductor software package. It contains the GENCODE version 40 annotation and ENCODE Registry of candidate cis-regulatory elements (cCREs) version 3. All for Human hg38 genome.

r-cftools 1.10.0
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-chipdbdata 1.0.0
Propagated dependencies: r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/yberda/ChIPDBData
Licenses: GPL 3
Build system: r
Synopsis: ChIP-seq Target Databases for TFEA.ChIP
Description:

This package provides curated gene target databases derived from ChIP-seq datasets, formatted as ChIPDB objects for use with TFEA.ChIP.

r-cellmigration 1.18.0
Propagated dependencies: r-vioplot@0.5.1 r-tiff@0.1-12 r-spatialtools@1.0.5 r-sp@2.2-0 r-reshape2@1.4.5 r-matrixstats@1.5.0 r-hmisc@5.2-4 r-foreach@1.5.2 r-fme@1.3.6.4 r-factominer@2.12 r-doparallel@1.0.17
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/ocbe-uio/cellmigRation/
Licenses: GPL 2
Build system: r
Synopsis: Track Cells, Analyze Cell Trajectories and Compute Migration Statistics
Description:

Import TIFF images of fluorescently labeled cells, and track cell movements over time. Parallelization is supported for image processing and for fast computation of cell trajectories. In-depth analysis of cell trajectories is enabled by 15 trajectory analysis functions.

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-ccimpute 1.12.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://github.com/khazum/ccImpute/
Licenses: GPL 3
Build system: r
Synopsis: ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)
Description:

Dropout events make the lowly expressed genes indistinguishable from true zero expression and different than the low expression present in cells of the same type. This issue makes any subsequent downstream analysis difficult. ccImpute is an imputation algorithm that uses cell similarity established by consensus clustering to impute the most probable dropout events in the scRNA-seq datasets. ccImpute demonstrated performance which exceeds the performance of existing imputation approaches while introducing the least amount of new noise as measured by clustering performance characteristics on datasets with known cell identities.

r-clariomsmousehttranscriptcluster-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/clariomsmousehttranscriptcluster.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix clariomsmouseht annotation data (chip clariomsmousehttranscriptcluster)
Description:

Affymetrix clariomsmouseht annotation data (chip clariomsmousehttranscriptcluster) assembled using data from public repositories.

r-csdr 1.16.0
Propagated dependencies: r-wgcna@1.73 r-rhpcblasctl@0.23-42 r-rcpp@1.1.0 r-matrixstats@1.5.0 r-glue@1.8.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: https://almaaslab.github.io/csdR
Licenses: GPL 3
Build system: r
Synopsis: Differential gene co-expression
Description:

This package contains functionality to run differential gene co-expression across two different conditions. The algorithm is inspired by Voigt et al. 2017 and finds Conserved, Specific and Differentiated genes (hence the name CSD). This package include efficient and variance calculation by bootstrapping and Welford's algorithm.

r-cosmiq 1.44.0
Propagated dependencies: r-xcms@4.8.0 r-rcpp@1.1.0 r-pracma@2.4.6 r-massspecwavelet@1.76.0 r-faahko@1.50.0
Channel: guix-bioc
Location: guix-bioc/packages/c.scm (guix-bioc packages c)
Home page: http://www.bioconductor.org/packages/devel/bioc/html/cosmiq.html
Licenses: GPL 3
Build system: r
Synopsis: cosmiq - COmbining Single Masses Into Quantities
Description:

cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step.

r-chicken-db 3.13.0
Propagated dependencies: r-org-gg-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/chicken.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix Chicken Array annotation data (chip chicken)
Description:

Affymetrix Affymetrix Chicken Array annotation data (chip chicken) assembled using data from public repositories.

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-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-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-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-compepitools 1.44.0
Propagated dependencies: r-xvector@0.50.0 r-topgo@2.62.0 r-seqinfo@1.0.0 r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-methylpipe@1.44.0 r-iranges@2.44.0 r-gplots@3.2.0 r-go-db@3.22.0 r-genomicranges@1.62.0 r-genomicfeatures@1.62.0 r-biostrings@2.78.0 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/compEpiTools
Licenses: GPL 2+ GPL 3+
Build system: r
Synopsis: Tools for computational epigenomics
Description:

This package provides tools for computational epigenomics developed for the analysis, integration and simultaneous visualization of various (epi)genomics data types across multiple genomic regions in multiple samples.

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Total results: 69112