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.

Last updated 24 days ago

differentialexpressiongeneexpressionmicroarrayreportwritingrnaseqsequencingvisualizationdifferential-expressioninteractive-visualizations

10.08 score 25 stars 2 packages 532 scripts 1.7k downloads

scPipe - 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.

Last updated 24 days ago

immunooncologysoftwaresequencingrnaseqgeneexpressionsinglecellvisualizationsequencematchingpreprocessingqualitycontrolgenomeannotationdataimport

9.20 score 68 stars 85 scripts 324 downloads

CellBench - 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.

Last updated 24 days ago

softwareinfrastructuresinglecellbenchmarkbioinformatics

8.68 score 29 stars 95 scripts 248 downloads

NanoMethViz - 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.

Last updated 24 days ago

softwarelongreadvisualizationdifferentialmethylationdnamethylationepigeneticsdataimport

7.00 score 24 stars 12 scripts 260 downloads