Guided construction of single cell reference

Notebook related to Su*, Zhou*, et al., Cell Stem Cell 2022 (PMID: 36332572)

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

A novel machine learning pipeline to analyse spatial transcriptomics data

R package to infer biological activities from omics data using a collection of methods.

Evaluation of the effect of quantification choices on RNA velocity estimates

A list of scRNA-seq analysis tools

The official home of the Presto distributed SQL query engine for big data

Bash scripts for Ibex users that install (or uninstall) Miniconda

Resources for processing and analyzing single-nuclei RNA-seq

Animate Anyone: Consistent and Controllable Image-to-Video Synthesis for Character Animation

The tidyverse style guide for R code

Authoring Books and Technical Documents with R Markdown

userChrome.css file for a Zotero dark theme. Suggestions for improvements are welcome.

The Modular Aligner and The Modular SV Caller

Single RNA-seq data analysis with R (Finland, May, 2019)

Learning the Variant Call Format

shell scripts and commands for whole genome analyses

SKATE R Utilities

A lightweight introduction to NextFlow, a workflow description language and engine for (mainly) bioinformatics workflows. Leverages notebooks for easy teaching.

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

MarcoPolo is a clustering-free approach to the exploration of bimodally expressed genes along with group information in single-cell RNA-seq data