Software

CellBench

R package for benchmarking single cell analysis methods

Github

Bioconductor

Publications

• CellBench: R/Bioconductor software for comparing single-cell RNA-seq analysis methods

EGSEA

Ensemble of Gene Set Enrichment Analyses

Github

Bioconductor

Publications

• Combining multiple tools outperforms individual methods in gene set enrichment analyses
• Easy and efficient ensemble gene set testing with EGSEA

FLAMES

A framework for performing single-cell and bulk read full-length analysis of mutations and splicing

Github

Bioconductor

Publications

• Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing

Glimma 2.0

An interactive R widget for creating plots for differential expression analysis

Github

Bioconductor

Publications

• Dashboard-style interactive plots for RNA-seq analysis are R Markdown ready with Glimma 2.0
• Glimma: interactive graphics for gene expression analysis

long-read-tools

A database of software tools for the analysis of long read sequencing data

Github

Publications

• long-read-tools.org: an interactive catalogue of analysis methods for long-read sequencing data
• Opportunities and challenges in long-read sequencing data analysis

NanoMethViz

Visualise methlation data from Oxford Nanopore sequencing

Github

Bioconductor

Publications

• NanoMethViz: An R/Bioconductor package for visualizing long-read methylation data

Restrander

A fast, accurate program for orienting and quality-checking cDNA sequencing reads.

Github

Publications

• Restrander: rapid orientation and artefact removal for long-read cDNA data

RNAseq123

R package that supports the F1000Research workflow article on RNA-seq analysis using limma, Glimma and edgeR

Github

Bioconductor

Publications

• RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

scPipe

R package that allows barcode demultiplexing, transcript counting and quality control of raw sequencing data from scRNA-seq and scATAC-seq datasets

Github

Bioconductor

Publications

• scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data
• scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor