Name: Yura Song
Type: User
Company: Université libre de Bruxelles
Bio: A bioinformatician in Cédric Blanpain lab. Mainly working on deciphering gene regulatory network on glandular epithelia.
Language: KR-EN-CN-FR-IT-NL
Twitter: yura__song
Location: Brussels, Belgium
Yura Song's Projects
Code Repository for Satpathy Granja et al 2019
ENCODE ATAC-seq pipeline
List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Materials presented at the BiocNYC meet-up
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
R package with motifs for use with chromVAR
Tools to process and analyze deep sequencing data.
A pixelclassification based multiplexed image segmentation pipeline
Lollipop-style mutation diagrams for annotating genetic variations.
MACS -- Model-based Analysis of ChIP-Seq
MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
mdlabbook is a markdown-format lab notebook
Midnight is a Jekyll theme for GitHub Pages
Course on analysis of NGS data (RNA-Seq. and ATAC-Seq.) using Galaxy
Quick mining and visualization of NGS data by integrating genomic databases
NicheNet: predict active ligand-target links between interacting cells
A code and script depository for the analysis in Blanpain Lab, regarding the project studying multipotency upon oncogenic stress
Use RMarkdown to generate PDF Conference Posters via HTML
Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
Template for project directory structure.
Codes for analysis and plotting on the paper
R notebook and example data for beginner :)
Toolkit for processing sequences in FASTA/Q formats
R toolkit for single cell genomics
a software package for analysis and exploration of single-cell RNA-seq datasets
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms