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.
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preprocessingsinglecellrnaseqatacseqdoubletssingle-cell
14.08 score 273 stars 3 dependents 2.5k scripts 8.6k downloadspipeComp - 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.
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geneexpressiontranscriptomicsclusteringdatarepresentationbenchmarkbioconductorpipeline-benchmarkingpipelinessingle-cell-rna-seq
7.56 score 44 stars 46 scripts 491 downloadssechm - 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.
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geneexpressionvisualization
7.30 score 8 stars 2 dependents 208 scripts 506 downloadsSEtools - 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).
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geneexpression
6.10 score 4 stars 105 scripts 463 downloadsscanMiR - 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).
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mirnasequencematchingalignment
5.93 score 1 dependents 71 scripts 428 downloadsepiwraps - epiwraps: Wrappers for plotting and dealing with epigenomics data
A set of wrappers to facilitate working with epigenomics data. Includes in particular wrappers for producing multitrack single-regions plots, enrichment heatmaps, bigwig generation, normalization, etc. The focus was put on a simple yet flexible interface.
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epigeneticssequencingnormalizationvisualization
5.87 score 210 scriptsdiffUTR - 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.
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geneexpression
5.70 score 7 stars 12 scripts 466 downloadsbetterChromVAR - Improved ChromVAR (Chromatin Variation Across Regions)
A much faster analytical implementation of chromVAR, with additional features, used to infer TF activity from (bulk or single-cell) ATAC-seq data and motif annotations (or binding probabilities). The package also includes the CVnorm normalization method based on the chromVAR logic.
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softwareatacseqnormalizationepigeneticssequencing
5.15 score 2 stars 1 scripts 330 downloadsscanMiRData - miRNA Affinity models for the scanMiR package
This package contains companion data to the scanMiR package. It contains `KdModel` (miRNA 12-mer binding affinity models) collections corresponding to all human, mouse and rat mirbase miRNAs. See the scanMiR package for details.
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mirnadataexperimentdatahomo_sapiens_datamus_musculus_datarattus_norvegicus_datadatapkg
5.09 score 1 dependents 41 scriptsscanMiRApp - 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.
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mirnasequencematchingguishinyapps
4.94 score 29 scripts 460 downloads