Glimma - Interactive visualizations for gene expression analysis
This package produces interactive visualizations for RNA-seq data analysis, utilizing output from limma, edgeR, or DESeq2. It produces interactive htmlwidgets versions of popular RNA-seq analysis plots to enhance the exploration of analysis results by overlaying interactive features. The plots can be viewed in a web browser or embedded in notebook documents.
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differentialexpressiongeneexpressionmicroarrayreportwritingrnaseqsequencingvisualizationdifferential-expressioninteractive-visualizations
10.85 score 35 stars 3 dependents 808 scripts 1.9k downloadsscPipe - Pipeline for single cell multi-omic data pre-processing
A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts from the fastq files and produces a feature count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.
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immunooncologysoftwaresequencingrnaseqgeneexpressionsinglecellvisualizationsequencematchingpreprocessingqualitycontrolgenomeannotationdataimportcurlbzip2xz-utilszlibcpp
9.25 score 67 stars 1 dependents 98 scripts 703 downloadsCellBench - Construct Benchmarks for Single Cell Analysis Methods
This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods.
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softwareinfrastructuresinglecellbenchmarkbioinformatics
9.06 score 33 stars 134 scripts 624 downloadsNanoMethViz - Visualise methylation data from Oxford Nanopore sequencing
NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.
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softwarelongreadvisualizationdifferentialmethylationdnamethylationepigeneticsdataimportzlibcpp
6.80 score 37 stars 19 scripts 581 downloads