Shen Lab at Mount Sinai

ngsplot

Quick mining and visualization of NGS data by integrating genomic databases

diffreps

Differential analysis for ChIP-seq with biological replicates

chip-seq_preprocess

A preprocessing pipeline for ChIP-seq, including alignment, quality control, and visualization.

region_analysis

A python script used to annotate genomic intervals.

GeneOverlap

R package for testing and visualizing gene list overlaps

ngsplotdb

Genome databases generation pipeline for ngs.plot and region_analysis.

DeepRegFinder

DeepRegFinder is a deep learning based program used to identify DNA regulatory elements using ChIP-seq

SPEctRA

A Scalable Pipeline for RNA‬‬‬-seq Ana‬‬lysis

pipelines_for_ChIP-seq_analysis

Pipelines for ChIP-seq analysis, such as peak calling, differential enrichment detection, and pausing index calculation for PolII.

NGS-Data-Charmer

This repository hosts an automated NGS data analysis (RNA-seq and ChIP-seq) pipeline created using Snakemake.

diffRepeats

Quantify repeat element enrichment with next-generation sequencing data

Gene-Attributes

A shiny app that obtains the coordinates and description of an input gene list (Ensembl v90) using biomaRt package.

miRNA_pipeline_for_miRanalyzer

A pipeline of miRNA by using miRanalyzer

RRHO2

Optimized RRHO2

software-best-practice

The best software engineering practices to develop bioinformatic programs

geneoverlap-old

R package for testing and visualizing gene overlaps

Isoseq_processing

RRHO_Modified.R

A slightly modified version of RRHO (http://www.bioconductor.org/packages/release/bioc/html/RRHO.html) which outputs common scale and enables 4 lists for RRHO compare.

shen-bioinfo-R

A collection of R code to perform bioinformatics.