Software

alpseq

An optimized software pipeline for processing sequencing data from nanobody libraries and panning campaigns

Github

Publications

• Alpseq: an open-source workflow to turbocharge nanobody discovery with high-throughput sequencing

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, spatial and bulk long-read pipeline for splicing and variant analysis

Github

Bioconductor

Publications

• Comprehensive characterization of single-cell full-length isoforms in human and mouse with long-read sequencing
• Igniting full-length isoform analysis in single-cell and spatial RNA-seq data with FLAMESv2

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

longmod123

An R/Bioconductor package that provides a comprehensive workflow for processing and analysing long-read DNA methylation data

Github

Publications

• Revised A streamlined workflow for long-read DNA methylation analysis with NanoMethViz and Bioconductor

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

matchbox

Rust-based read processing software that enables fluent manipulation and analysis of high-throughout sequencing data

Github

Publications

• Powerful read processing with matchbox

NAbseq

An accurate, rapid and cost-effective method for antibody long-read sequencing in hybridoma cell lines and single B cells

Github

Publications

• NAb-seq: an accurate, rapid, and cost-effective method for antibody long-read sequencing in hybridoma cell lines and single B cells

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

stPipe

An R/Bioconductor package that builds upon functionality in the scPipe software to allow preprocessing of spatial transcriptomics data

Github

Publications

• stPipe: A flexible and streamlined R/Bioconductor pipeline for preprocessing sequencing-based spatial transcriptomics data