Analysis scripts for the Vertesy 2018 paper: "Parental haplotype specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells"
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Updated
May 18, 2018 - R
Analysis scripts for the Vertesy 2018 paper: "Parental haplotype specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells"
A effort to collect all of the scRNA imputation methods and allow them to interface with scRNA-seq libraries (i. e. Seurat, SingleCellAssay, etc...)
adtseq provides simple Rcpp methods to identify Antibody-Derived-Tags in single cell CITE/REAP-seq data
scRNA-seq datasets to support Jung et al, Sci Adv, 7(6): eabe5735, 2021. DOI: 10.1126/sciadv.abe5735
Programming in practice based on RNA-seq, scRNA-seq, ATAC-seq, scATAC-seq or ChIP-seq.
Single-Cell Data Science
I've written a few functions that help me look through scRNA-seq data while working with Seurat.
Code for exploration of non-coding elements in single-cell RNA seq data
CHARGE Consortium: collaboration for mapping targets from 1000G GWAS on coronary artery calcification (CAC) with Maryam Kavousi, Maxime Bos, Clint L. Miller, and Pat Peyser.
A Snakemake workflow for performing and visualizing differential expression analyses (DEA) on NGS data powered by the R package limma.
ThunderBio scRNA-seq pipeline
Effect of temperature stress on Plasmodium Falciparum. Code for data analysis. Rshiny app for data exploration.
Graph Auto-Encoders (GAE) for Gene Regulatory Network (GRN) completion using scRNA-Seq datasets
This is a set of bash wrapper scripts for STAR that simplify it's setup and use with a set of pre-defined parameters.
scRNA-seq to analyze cells during human pluripotent stem cell differentiation into islets at D11, D14, D21, D32, D39.
Designing a framework to assess the performance of various tools in detecting HVGs in diverse datasets of scRNA-seq data in R
Single-Cell Data Analysis Tools
scCTS: identifying the cell type specific marker genes from population-level single-cell RNA-seq
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