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Platform Design Info for Affymetrix RabGene-1_1-st.
This package calculates probabilistic pathway scores using gene expression data. Gene expression values are aggregated into pathway-based scores using Bayesian network representations of biological pathways.
This package provides a package containing an environment representing the PrimeView.cdf file.
PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.
Platform Design Info for The Manufacturer's Name MG_U74A.
This package provides a package containing an environment representing the Poplar.cdf file.
Platform Design Info for Affymetrix RabGene-1_0-st.
This package provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV.
Platform Design Info for Affymetrix MarGene-1_0-st.
Platform Design Info for The Manufacturer's Name HG_U95A.
Platform Design Info for Affymetrix CyRGene-1_1-st.
Platform Design Info for Affymetrix GenomeWideSNP_5.
The package provides `rlang` data masks for the SummarizedExperiment class. The enables the evaluation of unquoted expression in different contexts of the SummarizedExperiment object with optional access to other contexts. The goal for `plyxp` is for evaluation to feel like a data.frame object without ever needing to unwind to a rectangular data.frame.
This package performs tests for paired high-throughput data.
Combine generalised least squares methodology from the nlme package for dealing with autocorrelation with penalised least squares methods from the glmnet package to deal with high dimensionality. This pengls packages glues them together through an iterative loop. The resulting method is applicable to high dimensional datasets that exhibit autocorrelation, such as spatial or temporal data.
This package contains all the datasets used in the PepsNMR package.
Platform Design Info for The Manufacturer's Name MG_U74Bv2.
Platform Design Info for Affymetrix EquGene-1_1-st.
Platform Design Info for Affymetrix HuGene-2_1-st.
Platform Design Info for The Manufacturer's Name Barley1.
This package provides methods and tools for (pre-)processing of metabolomics datasets (i.e. peak matrices), including filtering, normalisation, missing value imputation, scaling, and signal drift and batch effect correction methods. Filtering methods are based on: the fraction of missing values (across samples or features); Relative Standard Deviation (RSD) calculated from the Quality Control (QC) samples; the blank samples. Normalisation methods include Probabilistic Quotient Normalisation (PQN) and normalisation to total signal intensity. A unified user interface for several commonly used missing value imputation algorithms is also provided. Supported methods are: k-nearest neighbours (knn), random forests (rf), Bayesian PCA missing value estimator (bpca), mean or median value of the given feature and a constant small value. The generalised logarithm (glog) transformation algorithm is available to stabilise the variance across low and high intensity mass spectral features. Finally, this package provides an implementation of the Quality Control-Robust Spline Correction (QCRSC) algorithm for signal drift and batch effect correction of mass spectrometry-based datasets.
Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0).
Platform Design Info for The Manufacturer's Name Xenopus_laevis.
This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.