RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Plasmid annotation pipeline

Phigaro is a scalable command-line tool for predicting phages and prophages

Automated pipeline for analyses of fungal ITS from the Illumina

Tool for robust segmentation of >100 important anatomical structures in CT and MR images

Visualise correlation results and test significancies of these

Publication-ready volcano plots with enhanced colouring and labeling

PCAtools: everything Principal Components Analysis

A Bioconductor package and shiny app for DNA methylation data length bias adjustment in gene set testing

Tutorial for scRNA-seq data analysis beginners using R

EpiMethEx (Epigenetic Methylation and Expression), a R package to perform a large-scale integrated analysis by cyclic correlation analyses between methylation and gene expression data.

Batch effect adjustment based on negative binomial regression for RNA sequencing count data

An efficient FASTQ manipulation suite

Oxford Nanopore Technologies fast5 API software

a signal-level demultiplexer for Oxford Nanopore reads

qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

scLearn：Learning for single cell assignment

Discovering novel cell types across heterogenous single-cell experiments

SCSA: cell type annotation for single-cell RNA-seq data

A versatile sequenced read processor for nanopore direct RNA sequencing

DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets

DNA methylation analysis downstream to Nanopolish for Oxford Nanopore DNA sequencing datasets

LongQC is a tool for the data quality control of the PacBio and ONT long reads.

Inferring gene co-expression networks from single cell gene expression data

Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network out…

Extract modifed base call information from Guppy Fast5 files.

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)