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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-liebermanaidenhic2009 0.48.0
Propagated dependencies: r-kernsmooth@2.23-26 r-iranges@2.44.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/LiebermanAidenHiC2009
Licenses: LGPL 2.0+
Build system: r
Synopsis: Selected data from the HiC paper of E. Lieberman-Aiden et al. in Science (2009)
Description:

This package provides data that were presented in the article "Comprehensive mapping of long-range interactions reveals folding principles of the human genome", Science 2009 Oct 9;326(5950):289-93. PMID: 19815776.

r-legato 1.4.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://wejlab.github.io/LegATo-docs/
Licenses: Expat
Build system: r
Synopsis: LegATo: Longitudinal mEtaGenomic Analysis Toolkit
Description:

LegATo is a suite of open-source software tools for longitudinal microbiome analysis. It is extendable to several different study forms with optimal ease-of-use for researchers. Microbiome time-series data presents distinct challenges including complex covariate dependencies and variety of longitudinal study designs. This toolkit will allow researchers to determine which microbial taxa are affected over time by perturbations such as onset of disease or lifestyle choices, and to predict the effects of these perturbations over time, including changes in composition or stability of commensal bacteria.

r-lungcanceracvssccgeo 1.46.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: http://bioinformaticsprb.med.wayne.edu/
Licenses: GPL 2
Build system: r
Synopsis: lung cancer dataset that can be used with maPredictDSC package for developing outcome prediction models from Affymetrix CEL files.
Description:

This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580).

r-lumibarnes 1.50.0
Propagated dependencies: r-lumi@2.62.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/lumiBarnes
Licenses: LGPL 2.0+
Build system: r
Synopsis: Barnes Benchmark Illumina Tissues Titration Data
Description:

The Barnes benchmark dataset can be used to evaluate the algorithms for Illumina microarrays. It measured a titration series of two human tissues, blood and placenta, and includes six samples with the titration ratio of blood and placenta as 100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate. The data is loaded as an LumiBatch Object (see documents in the lumi package).

r-looking4clusters 1.0.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-singlecellexperiment@1.32.0 r-jsonlite@2.0.0 r-biocbaseutils@1.12.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://github.com/BioinfoUSAL/looking4clusters/
Licenses: GPL 2 GPL 3
Build system: r
Synopsis: Interactive Visualization of scRNA-Seq
Description:

Enables the interactive visualization of dimensional reduction, clustering, and cell properties for scRNA-Seq results. It generates an interactive HTML page using either a numeric matrix, SummarizedExperiment, SingleCellExperiment or Seurat objects as input. The input data can be projected into two-dimensional representations by applying dimensionality reduction methods such as PCA, MDS, t-SNE, UMAP, and NMF. Displaying multiple dimensionality reduction results within the same interface, with interconnected graphs, provides different perspectives that facilitate accurate cell classification. The package also integrates unsupervised clustering techniques, whose results that can be viewed interactively in the graphical interface. In addition to visualization, this interface allows manual selection of groups, labeling of cell entities based on processed meta-information, generation of new graphs displaying gene expression values for each cell, sample identification, and visual comparison of samples and clusters.

r-lipidr 2.24.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://github.com/ahmohamed/lipidr
Licenses: Expat
Build system: r
Synopsis: Data Mining and Analysis of Lipidomics Datasets
Description:

lipidr an easy-to-use R package implementing a complete workflow for downstream analysis of targeted and untargeted lipidomics data. lipidomics results can be imported into lipidr as a numerical matrix or a Skyline export, allowing integration into current analysis frameworks. Data mining of lipidomics datasets is enabled through integration with Metabolomics Workbench API. lipidr allows data inspection, normalization, univariate and multivariate analysis, displaying informative visualizations. lipidr also implements a novel Lipid Set Enrichment Analysis (LSEA), harnessing molecular information such as lipid class, total chain length and unsaturation.

r-limrots 1.2.8
Propagated dependencies: r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-s4vectors@0.48.0 r-qvalue@2.42.0 r-limma@3.66.0 r-dplyr@1.1.4 r-biocparallel@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://github.com/AliYoussef96/LimROTS
Licenses: GPL 2+
Build system: r
Synopsis: LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis
Description:

Differential expression analysis is a prevalent method utilised in the examination of diverse biological data. The reproducibility-optimized test statistic (ROTS) modifies a t-statistic based on the data's intrinsic characteristics and ranks features according to their statistical significance for differential expression between two or more groups (f-statistic). Focussing on proteomics and metabolomics, the current ROTS implementation cannot account for technical or biological covariates such as MS batches or gender differences among the samples. Consequently, we developed LimROTS, which employs a reproducibility-optimized test statistic utilising the limma methodology to simulate complex experimental designs. LimROTS is a hybrid method integrating empirical bayes and reproducibility-optimized statistics for robust analysis of proteomics and metabolomics data.

r-limmagui 1.86.0
Propagated dependencies: r-xtable@1.8-4 r-tkrplot@0.0-30 r-r2html@2.3.4 r-limma@3.66.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: http://bioinf.wehi.edu.au/limmaGUI/
Licenses: FSDG-compatible
Build system: r
Synopsis: GUI for limma Package With Two Color Microarrays
Description:

This package provides a Graphical User Interface for differential expression analysis of two-color microarray data using the limma package.

r-listeretalbsseq 1.42.0
Propagated dependencies: r-methylpipe@1.44.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/ListerEtAlBSseq
Licenses: FSDG-compatible
Build system: r
Synopsis: BS-seq data of H1 and IMR90 cell line excerpted from Lister et al. 2009
Description:

Base resolution bisulfite sequencing data of Human DNA methylomes.

r-lungexpression 0.48.0
Propagated dependencies: r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/lungExpression
Licenses: GPL 2+
Build system: r
Synopsis: ExpressionSets for Parmigiani et al., 2004 Clinical Cancer Research paper
Description:

Data from three large lung cancer studies provided as ExpressionSets.

r-lheuristic 1.2.0
Propagated dependencies: r-multiassayexperiment@1.36.1 r-hmisc@5.2-4 r-ggpubr@0.6.2 r-ggplot2@4.0.1 r-energy@1.7-12
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://github.com/ASPresearch/Lheuristic
Licenses: Expat
Build system: r
Synopsis: Detection of scatterplots with L-shaped pattern
Description:

The Lheuristic package identifies scatterpots that follow and L-shaped, negative distribution. It can be used to identify genes regulated by methylation by integration of an expression and a methylation array. The package uses two different methods to detect expression and methyaltion L- shapped scatterplots. The parameters can be changed to detect other scatterplot patterns.

r-lumiratall-db 1.22.0
Propagated dependencies: r-org-rn-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/lumiRatAll.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina Rat Illumina expression annotation data (chip lumiRatAll)
Description:

Illumina Rat Illumina expression annotation data (chip lumiRatAll) assembled using data from public repositories.

r-lemur 1.8.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://github.com/const-ae/lemur
Licenses: Expat
Build system: r
Synopsis: Latent Embedding Multivariate Regression
Description:

Fit a latent embedding multivariate regression (LEMUR) model to multi-condition single-cell data. The model provides a parametric description of single-cell data measured with treatment vs. control or more complex experimental designs. The parametric model is used to (1) align conditions, (2) predict log fold changes between conditions for all cells, and (3) identify cell neighborhoods with consistent log fold changes. For those neighborhoods, a pseudobulked differential expression test is conducted to assess which genes are significantly changed.

r-linkset 1.0.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://github.com/GilbertHan1011/linkSet
Licenses: Expat
Build system: r
Synopsis: Base Classes for Storing Genomic Link Data
Description:

This package provides a comprehensive framework for representing, analyzing, and visualizing genomic interactions, particularly focusing on gene-enhancer relationships. The package extends the GenomicRanges infrastructure to handle paired genomic regions with specialized methods for chromatin interaction data from Hi-C, Promoter Capture Hi-C (PCHi-C), and single-cell ATAC-seq experiments. Key features include conversion from common interaction formats, annotation of promoters and enhancers, distance-based analyses, interaction strength metrics, statistical modeling using CHiCANE methodology, and tailored visualization tools. The package aims to standardize the representation of genomic interaction data while providing domain-specific functions not available in general genomic interaction packages.

r-limpa 1.2.5
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://github.com/SmythLab/limpa
Licenses: FSDG-compatible
Build system: r
Synopsis: Quantification and Differential Analysis of Proteomics Data
Description:

Quantification and differential analysis of mass-spectrometry proteomics data, with probabilistic recovery of information from missing values. Avoids the need for imputation. Estimates the detection probability curve (DPC), which relates the probability of successful detection to the underlying log-intensity of each precursor ion, and uses it to incorporate missing values into protein quantification and into subsequent differential expression analyses. The package produces objects suitable for downstream analysis in limma. The package accepts precursor (or peptide) intensities including missing values and produces complete protein quantifications without the need for imputation. The uncertainty of the protein quantifications is propagated through to the limma analyses using variance modeling and precision weights, ensuring accurate error rate control. The analysis pipeline can alternatively work with PTM or protein level data. The package name "limpa" is an acronym for "Linear Models for Proteomics Data".

r-lrbasedbi 2.20.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/LRBaseDbi
Licenses: Artistic License 2.0
Build system: r
Synopsis: DBI to construct LRBase-related package
Description:

Interface to construct LRBase package (LRBase.XXX.eg.db).

r-lymphoseqdb 0.99.2
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/LymphoSeqDB
Licenses: Artistic License 2.0
Build system: r
Synopsis: LymphoSeq annotation databases
Description:

This package provides annotation databases that support the package LymphoSeq.

r-loomexperiment 1.28.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-singlecellexperiment@1.32.0 r-s4vectors@0.48.0 r-rhdf5@2.54.0 r-matrix@1.7-4 r-hdf5array@1.38.0 r-genomicranges@1.62.0 r-delayedarray@0.36.0 r-biocio@1.20.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/LoomExperiment
Licenses: Artistic License 2.0
Build system: r
Synopsis: LoomExperiment container
Description:

The LoomExperiment package provide a means to easily convert the Bioconductor "Experiment" classes to loom files and vice versa.

r-leebamviews 1.46.0
Propagated dependencies: r-s4vectors@0.48.0 r-rsamtools@2.26.0 r-iranges@2.44.0 r-genomicranges@1.62.0 r-genomicalignments@1.46.0 r-bsgenome@1.78.0 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/leeBamViews
Licenses: FSDG-compatible
Build system: r
Synopsis: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009
Description:

data from PMID 19096707; prototype for managing multiple NGS samples.

r-lumimouseall-db 1.22.0
Propagated dependencies: r-org-mm-eg-db@3.22.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/lumiMouseAll.db
Licenses: Artistic License 2.0
Build system: r
Synopsis: Illumina Mouse Illumina expression annotation data (chip lumiMouseAll)
Description:

Illumina Mouse Illumina expression annotation data (chip lumiMouseAll) assembled using data from public repositories.

r-les 1.60.0
Propagated dependencies: r-rcolorbrewer@1.1-3 r-gplots@3.2.0 r-fdrtool@1.2.18 r-boot@1.3-32
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/les
Licenses: GPL 3
Build system: r
Synopsis: Identifying Differential Effects in Tiling Microarray Data
Description:

The les package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.

r-liquidassociation 1.64.0
Propagated dependencies: r-yeastcc@1.50.0 r-org-sc-sgd-db@3.22.0 r-geepack@1.3.13 r-biobase@2.70.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/LiquidAssociation
Licenses: GPL 3+
Build system: r
Synopsis: LiquidAssociation
Description:

The package contains functions for calculate direct and model-based estimators for liquid association. It also provides functions for testing the existence of liquid association given a gene triplet data.

r-lbe 1.78.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/LBE
Licenses: GPL 2
Build system: r
Synopsis: Estimation of the false discovery rate
Description:

LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis.

r-lionessr 1.24.0
Propagated dependencies: r-summarizedexperiment@1.40.0 r-s4vectors@0.48.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://github.com/mararie/lionessR
Licenses: Expat
Build system: r
Synopsis: Modeling networks for individual samples using LIONESS
Description:

LIONESS, or Linear Interpolation to Obtain Network Estimates for Single Samples, can be used to reconstruct single-sample networks (https://arxiv.org/abs/1505.06440). This code implements the LIONESS equation in the lioness function in R to reconstruct single-sample networks. The default network reconstruction method we use is based on Pearson correlation. However, lionessR can run on any network reconstruction algorithms that returns a complete, weighted adjacency matrix. lionessR works for both unipartite and bipartite networks.

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Total results: 69112