Yura Song's repositories
ImcSegmentationPipeline
A pixelclassification based multiplexed image segmentation pipeline
project-template
Template for project directory structure.
10x-scATAC-2019
Code Repository for Satpathy Granja et al 2019
atac-seq-pipeline
ENCODE ATAC-seq pipeline
awesome-single-cell
List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
BiocNYC
Materials presented at the BiocNYC meet-up
bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
CellphoneDB
CellPhoneDB can be used to search for a particular ligand/receptor, or interrogate your own HUMAN single-cell transcriptomics data.
chromVARmotifs
R package with motifs for use with chromVAR
deepTools
Tools to process and analyze deep sequencing data.
lollipops
Lollipop-style mutation diagrams for annotating genetic variations.
MACS
MACS -- Model-based Analysis of ChIP-Seq
MAGIC
MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
mdlabbook
mdlabbook is a markdown-format lab notebook
midnight
Midnight is a Jekyll theme for GitHub Pages
NGS_Course
Course on analysis of NGS data (RNA-Seq. and ATAC-Seq.) using Galaxy
nichenetr
NicheNet: predict active ligand-target links between interacting cells
Pik3ca_MG_analysis
A code and script depository for the analysis in Blanpain Lab, regarding the project studying multipotency upon oncogenic stress
posterdown
Use RMarkdown to generate PDF Conference Posters via HTML
powsimR
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.
PTEN_codes
Codes for analysis and plotting on the paper
R-coursework
R notebook and example data for beginner :)
seqtk
Toolkit for processing sequences in FASTA/Q formats
seurat
R toolkit for single cell genomics
Severo.jl
a software package for analysis and exploration of single-cell RNA-seq datasets
vcf2maf
Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms