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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-hspec 0.99.1
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/Hspec
Licenses: LGPL 2.0+
Build system: r
Synopsis: Hspec
Description:

This package provides a package containing an environment representing the HGU133Plus2_Hs_Hspec.cdf file.

r-heatmaps 1.34.0
Propagated dependencies: r-seqinfo@1.0.0 r-rcolorbrewer@1.1-3 r-plotrix@3.8-13 r-matrix@1.7-4 r-kernsmooth@2.23-26 r-iranges@2.44.0 r-genomicranges@1.62.0 r-ebimage@4.52.0 r-biostrings@2.78.0 r-biocgenerics@0.56.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/heatmaps
Licenses: Artistic License 2.0
Build system: r
Synopsis: Flexible Heatmaps for Functional Genomics and Sequence Features
Description:

This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.

r-hgu133a2-db 3.13.0
Propagated dependencies: r-org-hs-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/hgu133a2.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix HG-U133A_2 Array annotation data (chip hgu133a2)
Description:

Affymetrix Affymetrix HG-U133A_2 Array annotation data (chip hgu133a2) assembled using data from public repositories.

r-hgug4845a-db 0.0.3
Propagated dependencies: r-org-hs-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/hgug4845a.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: agilent AMADID 026652 annotation data (chip hgug4845a)
Description:

agilent AMADID 026652 annotation data (chip hgug4845a) assembled using data from public repositories.

r-hu6800cdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/hu6800cdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: hu6800cdf
Description:

This package provides a package containing an environment representing the Hu6800.CDF file.

r-hvp 1.0.0
Propagated dependencies: r-matrix@1.7-4
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/HVP
Licenses: Expat
Build system: r
Synopsis: Hierarchical Variance Partitioning
Description:

HVP is a quantitative batch effect metric that estimates the proportion of variance associated with batch effects in a data set.

r-highlyreplicatedrnaseq 1.22.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0 r-experimenthub@3.0.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://github.com/const-ae/HighlyReplicatedRNASeq
Licenses: Expat
Build system: r
Synopsis: Collection of Bulk RNA-Seq Experiments With Many Replicates
Description:

Gene-level count matrix data for bulk RNA-seq dataset with many replicates. The data are provided as easy to use SummarizedExperiment objects. The source data that is made accessible through this package comes from https://github.com/bartongroup/profDGE48.

r-hgu95dcdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/hgu95dcdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: hgu95dcdf
Description:

This package provides a package containing an environment representing the HG_U95D.CDF file.

r-hicpotts 1.0.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://github.com/igosungithub/HiCPotts
Licenses: GPL 3
Build system: r
Synopsis: HiCPotts: Hierarchical Modeling to Identify and Correct Genomic Biases in Hi-C
Description:

The HiCPotts package provides a comprehensive Bayesian framework for analyzing Hi-C interaction data, integrating both spatial and genomic biases within a probabilistic modeling framework. At its core, HiCPotts leverages the Potts model (Wu, 1982)—a well-established graphical model—to capture and quantify spatial dependencies across interaction loci arranged on a genomic lattice. By treating each interaction as a spatially correlated random variable, the Potts model enables robust segmentation of the genomic landscape into meaningful components, such as noise, true signals, and false signals. To model the influence of various genomic biases, HiCPotts employs a regression-based approach incorporating multiple covariates: Genomic distance (D): The distance between interacting loci, recognized as a fundamental driver of contact frequency. GC-content (GC): The local GC composition around the interacting loci, which can influence chromatin structure and interaction patterns. Transposable elements (TEs): The presence and abundance of repetitive elements that may shape contact probability through chromatin organization. Accessibility score (Acc): A measure of chromatin openness, informing how accessible certain genomic regions are to interaction. By embedding these covariates into a hierarchical mixture model, HiCPotts characterizes each interaction’s probability of belonging to one of several latent components. The model parameters, including regression coefficients, zero-inflation parameters (for ZIP/ZINB distributions), and dispersion terms (for NB/ZINB distributions), are inferred via a MCMC sampler. This algorithm draws samples from the joint posterior distribution, allowing for flexible posterior inference on model parameters and hidden states. From these posterior samples, HiCPotts computes posterior means of regression parameters and other quantities of interest. These posterior estimates are then used to calculate the posterior probabilities that assign each interaction to a specific component. The resulting classification sheds light on the underlying structure: distinguishing genuine high-confidence interactions (signal) from background noise and potential false signals, while simultaneously quantifying the impact of genomic biases on observed interaction frequencies. In summary, HiCPotts seamlessly integrates spatial modeling, bias correction, and probabilistic classification into a unified Bayesian inference framework. It provides rich posterior summaries and interpretable, model-based assignments of interaction states, enabling researchers to better understand the interplay between genomic organization, biases, and spatial correlation in Hi-C data.

r-heebodata 1.48.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/HEEBOdata
Licenses: LGPL 2.0+
Build system: r
Synopsis: HEEBO set and HEEBO controls
Description:

R objects describing the HEEBO oligo set.

r-htmg430b-db 3.13.0
Propagated dependencies: r-org-mm-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/htmg430b.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix Affymetrix HT_MG-430B Array annotation data (chip htmg430b)
Description:

Affymetrix Affymetrix HT_MG-430B Array annotation data (chip htmg430b) assembled using data from public repositories.

r-hippo 1.22.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://github.com/tk382/HIPPO
Licenses: FSDG-compatible
Build system: r
Synopsis: Heterogeneity-Induced Pre-Processing tOol
Description:

For scRNA-seq data, it selects features and clusters the cells simultaneously for single-cell UMI data. It has a novel feature selection method using the zero inflation instead of gene variance, and computationally faster than other existing methods since it only relies on PCA+Kmeans rather than graph-clustering or consensus clustering.

r-human-db0 3.22.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/human.db0
Licenses: Artistic License 2.0
Build system: r
Synopsis: Base Level Annotation databases for human
Description:

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

r-humanaffydata 1.36.0
Propagated dependencies: r-experimenthub@3.0.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/HumanAffyData
Licenses: Artistic License 2.0
Build system: r
Synopsis: GEO accession GSE64985 and ArrayExpress accession E-MTAB-62 as ExpressionSet objects
Description:

Re-analysis of human gene expression data generated on the Affymetrix HG_U133PlusV2 (EH176) and Affymetrix HG_U133A (EH177) platforms. The original data were normalized using robust multiarray averaging (RMA) to obtain an integrated gene expression atlas across diverse biological sample types and conditions. The entire compendia comprisee 9395 arrays for EH176 and 5372 arrays for EH177.

r-htmg430pmcdf 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/htmg430pmcdf
Licenses: LGPL 2.0+
Build system: r
Synopsis: htmg430pmcdf
Description:

This package provides a package containing an environment representing the HT_MG-430_PM.cdf file.

r-hilbertvis 1.68.0
Propagated dependencies: r-lattice@0.22-7
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: http://www.ebi.ac.uk/~anders/hilbert
Licenses: GPL 3+
Build system: r
Synopsis: Hilbert curve visualization
Description:

This package provides functions to visualize long vectors of integer data by means of Hilbert curves.

r-hguqiagenv3-db 3.2.3
Propagated dependencies: r-org-hs-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/hguqiagenv3.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Qiagen Qiagen V3.0 oligo set annotation data (chip hguqiagenv3)
Description:

Qiagen Qiagen V3.0 oligo set annotation data (chip hguqiagenv3) assembled using data from public repositories.

r-human650v3acrlmm 1.0.3
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/human650v3aCrlmm
Licenses: Artistic License 2.0
Build system: r
Synopsis: Metadata for fast genotyping with the 'crlmm' package
Description:

Package with metadata for genotyping Illumina 650k arrays using the crlmm package.

r-herper 1.20.0
Propagated dependencies: r-withr@3.0.2 r-rjson@0.2.23 r-reticulate@1.44.1
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://github.com/RockefellerUniversity/Herper
Licenses: GPL 3
Build system: r
Synopsis: The Herper package is a simple toolset to install and manage conda packages and environments from R
Description:

Many tools for data analysis are not available in R, but are present in public repositories like conda. The Herper package provides a comprehensive set of functions to interact with the conda package managament system. With Herper users can install, manage and run conda packages from the comfort of their R session. Herper also provides an ad-hoc approach to handling external system requirements for R packages. For people developing packages with python conda dependencies we recommend using basilisk (https://bioconductor.org/packages/release/bioc/html/basilisk.html) to internally support these system requirments pre-hoc.

r-hireewas 1.28.0
Propagated dependencies: r-quadprog@1.5-8 r-gplots@3.2.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/HIREewas
Licenses: GPL 2+
Build system: r
Synopsis: Detection of cell-type-specific risk-CpG sites in epigenome-wide association studies
Description:

In epigenome-wide association studies, the measured signals for each sample are a mixture of methylation profiles from different cell types. The current approaches to the association detection only claim whether a cytosine-phosphate-guanine (CpG) site is associated with the phenotype or not, but they cannot determine the cell type in which the risk-CpG site is affected by the phenotype. We propose a solid statistical method, HIgh REsolution (HIRE), which not only substantially improves the power of association detection at the aggregated level as compared to the existing methods but also enables the detection of risk-CpG sites for individual cell types. The "HIREewas" R package is to implement HIRE model in R.

r-hgug4111a-db 3.2.3
Propagated dependencies: r-org-hs-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/hgug4111a.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Agilent Human 1B annotation data (chip hgug4111a)
Description:

Agilent Human 1B annotation data (chip hgug4111a) assembled using data from public repositories.

r-hgu2beta7 1.50.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/hgu2beta7
Licenses: Artistic License 2.0
Build system: r
Synopsis: data package containing annotation data for hgu2beta7
Description:

Annotation data file for hgu2beta7 assembled using data from public data repositories.

r-hugene20stprobeset-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/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/hugene20stprobeset.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Affymetrix hugene20 annotation data (chip hugene20stprobeset)
Description:

Affymetrix hugene20 annotation data (chip hugene20stprobeset) assembled using data from public repositories.

r-hthgu133bprobe 2.18.0
Propagated dependencies: r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/h.scm (guix-bioc packages h)
Home page: https://bioconductor.org/packages/hthgu133bprobe
Licenses: LGPL 2.0+
Build system: r
Synopsis: Probe sequence data for microarrays of type hthgu133b
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 HT\_HG-U133B\_probe\_tab.

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Total results: 69112