Jiantao Shi's repositories
MoranProcess
Characterizing cancer initiation by Moran Process
AML-InVivo-CRISPR
In vivo genome-wide CRISPR screening in murine acute myeloid leukemia
Clipper
A p-value-free method for controlling false discovery rates in high-throughput biological data with two conditions
dit
Python package for information theory.
EPEE
Effector and Perturbation Estimation Engine (EPEE) conducts differential analysis of transcription factor activity from gene expression data.
iab2
An Introduction to Applied Bioinformatics, 2nd Edition
IMPACT-Pipeline
Framework to process and call somatic variation from NGS dataset generated using MSK-IMPACT assay
LungMR
Master regulators in LUAD
MONOD2
MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data
RIL-seq-interacting-regions
A simple tool to calculate accurate genome interacting regions based on RIL-seq
scAge
Profiling epigenetic age in single cells
single-cell-tutorial
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
TRAmHap
TRAmHap is a novel deep-learning framework, which predicts transcriptional activity using characteristics of DNA methylation haplotypes in proximal promoters and enhancers as far as 25 kb away from TSS.