scDblFinder - scDblFinder
The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly found in the scran package, the new fast and comprehensive scDblFinder method, and a reimplementation of the Amulet detection method for single-cell ATAC-seq.
Last updated 3 months ago
preprocessingsinglecellrnaseqatacseq
148 stars 5.18 score 119 dependencies 1 dependentspipeComp - pipeComp pipeline benchmarking framework
A simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.
Last updated 4 months ago
geneexpressiontranscriptomicsclusteringdatarepresentation
40 stars 2.83 score 208 dependenciesscanMiR - scanMiR
A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. It supports scanning using miRNA seeds, full miRNA sequences (enabling 3' alignment) and KdModels, and includes the prediction of slicing and TDMD sites. Finally, it includes utility and plotting functions (e.g. for the visual representation of miRNA-target alignment).
Last updated 2 months ago
mirnasequencematchingalignment
1.45 score 60 dependencies 1 dependentssechm - sechm: Complex Heatmaps from a SummarizedExperiment
sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package. It enables plotting annotated heatmaps from SE objects, with easy access to rowData and colData columns, and implements a number of features to make the generation of heatmaps easier and more flexible. These functionalities used to be part of the SEtools package.
Last updated 3 months ago
geneexpressionvisualization
1.08 score 72 dependencies 2 dependentsdiffUTR - diffUTR: Streamlining differential exon and 3' UTR usage
The diffUTR package provides a uniform interface and plotting functions for limma/edgeR/DEXSeq -powered differential bin/exon usage. It includes in addition an improved version of the limma::diffSplice method. Most importantly, diffUTR further extends the application of these frameworks to differential UTR usage analysis using poly-A site databases.
Last updated 4 months ago
geneexpression
0.82 score 135 dependenciesSEtools - SEtools: tools for working with SummarizedExperiment
This includes a set of convenience functions for working with the SummarizedExperiment class. Note that plotting functions historically in this package have been moved to the sechm package (see vignette for details).
Last updated 4 months ago
geneexpression
2 stars 0.82 score 118 dependenciesscanMiRApp - scanMiR shiny application
A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.
Last updated 4 months ago
mirnasequencematchingguishinyapps
0.23 score 151 dependencies