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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-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-lmdme 1.52.0
Propagated dependencies: r-stemhypoxia@1.46.0 r-pls@2.8-5 r-limma@3.66.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: http://www.bdmg.com.ar/?page_id=38
Licenses: FSDG-compatible
Build system: r
Synopsis: Linear Model decomposition for Designed Multivariate Experiments
Description:

linear ANOVA decomposition of Multivariate Designed Experiments implementation based on limma lmFit. Features: i)Flexible formula type interface, ii) Fast limma based implementation, iii) p-values for each estimated coefficient levels in each factor, iv) F values for factor effects and v) plotting functions for PCA and PLS.

r-lumimouseidmapping 1.10.0
Propagated dependencies: r-lumi@2.62.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/lumiMouseIDMapping
Licenses: FSDG-compatible
Build system: r
Synopsis: Illumina Identifier mapping for Mouse
Description:

This package includes mappings information between different types of Illumina IDs of Illumina Mouse chips and nuIDs. It also includes mappings of all nuIDs included in Illumina Mouse chips to RefSeq IDs with mapping qualities information.

r-lydata 1.36.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/lydata
Licenses: Expat
Build system: r
Synopsis: Example Dataset for crossmeta Package
Description:

Raw data downloaded from GEO for the compound LY294002. Raw data is from multiple platforms from Affymetrix and Illumina. This data is used to illustrate the cross-platform meta-analysis of microarray data using the crossmeta package.

r-lymphoseq 1.38.0
Propagated dependencies: r-venndiagram@1.7.3 r-upsetr@1.4.0 r-stringdist@0.9.15 r-reshape@0.8.10 r-rcolorbrewer@1.1-3 r-plyr@1.8.9 r-phangorn@2.12.1 r-msa@1.42.0 r-lymphoseqdb@0.99.2 r-ineq@0.2-13 r-ggtree@4.0.1 r-ggplot2@4.0.1 r-dplyr@1.1.4 r-data-table@1.17.8 r-circlize@0.4.16 r-biostrings@2.78.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/LymphoSeq
Licenses: Artistic License 2.0
Build system: r
Synopsis: Analyze high-throughput sequencing of T and B cell receptors
Description:

This R package analyzes high-throughput sequencing of T and B cell receptor complementarity determining region 3 (CDR3) sequences generated by Adaptive Biotechnologies ImmunoSEQ assay. Its input comes from tab-separated value (.tsv) files exported from the ImmunoSEQ analyzer.

r-lace 2.14.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://github.com/BIMIB-DISCo/LACE
Licenses: FSDG-compatible
Build system: r
Synopsis: Longitudinal Analysis of Cancer Evolution (LACE)
Description:

LACE is an algorithmic framework that processes single-cell somatic mutation profiles from cancer samples collected at different time points and in distinct experimental settings, to produce longitudinal models of cancer evolution. The approach solves a Boolean Matrix Factorization problem with phylogenetic constraints, by maximizing a weighed likelihood function computed on multiple time points.

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-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-lpe 1.84.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: http://www.r-project.org
Licenses: LGPL 2.0+
Build system: r
Synopsis: Methods for analyzing microarray data using Local Pooled Error (LPE) method
Description:

This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional BH or BY procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library.

r-lobstahs 1.36.0
Propagated dependencies: r-xcms@4.8.0 r-camera@1.66.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: http://bioconductor.org/packages/LOBSTAHS
Licenses: FSDG-compatible
Build system: r
Synopsis: Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences
Description:

LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment.

r-logicfs 2.30.0
Propagated dependencies: r-survival@3.8-3 r-mcbiopi@1.1.7 r-logicreg@1.6.6
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/logicFS
Licenses: LGPL 2.0+
Build system: r
Synopsis: Identification of SNP Interactions
Description:

Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification.

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-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-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-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-lisaclust 1.18.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://ellispatrick.github.io/lisaClust/
Licenses: FSDG-compatible
Build system: r
Synopsis: lisaClust: Clustering of Local Indicators of Spatial Association
Description:

lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.

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-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-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-lumiratidmapping 1.10.0
Propagated dependencies: r-lumi@2.62.0 r-annotationdbi@1.72.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://bioconductor.org/packages/lumiRatIDMapping
Licenses: FSDG-compatible
Build system: r
Synopsis: Illumina Identifier mapping for Rat
Description:

This package includes mappings information between different types of Illumina IDs of Illumina Rat chips and nuIDs. It also includes mappings of all nuIDs included in Illumina Rat chips to RefSeq IDs with mapping qualities information.

r-limpca 1.6.0
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://github.com/ManonMartin/limpca
Licenses: Artistic License 2.0
Build system: r
Synopsis: An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family of methods
Description:

This package has for objectives to provide a method to make Linear Models for high-dimensional designed data. limpca applies a GLM (General Linear Model) version of ASCA and APCA to analyse multivariate sample profiles generated by an experimental design. ASCA/APCA provide powerful visualization tools for multivariate structures in the space of each effect of the statistical model linked to the experimental design and contrarily to MANOVA, it can deal with mutlivariate datasets having more variables than observations. This method can handle unbalanced design.

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-lineagespot 1.14.0
Propagated dependencies: r-variantannotation@1.56.0 r-summarizedexperiment@1.40.0 r-stringr@1.6.0 r-matrixgenerics@1.22.0 r-httr@1.4.7 r-data-table@1.17.8
Channel: guix-bioc
Location: guix-bioc/packages/l.scm (guix-bioc packages l)
Home page: https://github.com/BiodataAnalysisGroup/lineagespot
Licenses: Expat
Build system: r
Synopsis: Detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing
Description:

Lineagespot is a framework written in R, and aims to identify SARS-CoV-2 related mutations based on a single (or a list) of variant(s) file(s) (i.e., variant calling format). The method can facilitate the detection of SARS-CoV-2 lineages in wastewater samples using next generation sequencing, and attempts to infer the potential distribution of the SARS-CoV-2 lineages.

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.

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Total results: 69112