Stars
Scripts and documentations on the MCSC decontamination method
A tool to extract variable regions from 16S gene sequences
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
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
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
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…