Pinned Repositories
chip-seq_preprocess
A preprocessing pipeline for ChIP-seq, including alignment, quality control, and visualization.
DeepRegFinder
DeepRegFinder is a deep learning based program used to identify DNA regulatory elements using ChIP-seq
diffreps
Differential analysis for ChIP-seq with biological replicates
GeneOverlap
R package for testing and visualizing gene list overlaps
NGS-Data-Charmer
This repository hosts an automated NGS data analysis (RNA-seq and ChIP-seq) pipeline created using Snakemake.
ngsplot
Quick mining and visualization of NGS data by integrating genomic databases
ngsplotdb
Genome databases generation pipeline for ngs.plot and region_analysis.
pipelines_for_ChIP-seq_analysis
Pipelines for ChIP-seq analysis, such as peak calling, differential enrichment detection, and pausing index calculation for PolII.
region_analysis
A python script used to annotate genomic intervals.
SPEctRA
A Scalable Pipeline for RNA-seq Analysis
Shen Lab at Mount Sinai's Repositories
shenlab-sinai/ngsplot
Quick mining and visualization of NGS data by integrating genomic databases
shenlab-sinai/diffreps
Differential analysis for ChIP-seq with biological replicates
shenlab-sinai/chip-seq_preprocess
A preprocessing pipeline for ChIP-seq, including alignment, quality control, and visualization.
shenlab-sinai/region_analysis
A python script used to annotate genomic intervals.
shenlab-sinai/GeneOverlap
R package for testing and visualizing gene list overlaps
shenlab-sinai/ngsplotdb
Genome databases generation pipeline for ngs.plot and region_analysis.
shenlab-sinai/DeepRegFinder
DeepRegFinder is a deep learning based program used to identify DNA regulatory elements using ChIP-seq
shenlab-sinai/SPEctRA
A Scalable Pipeline for RNA-seq Analysis
shenlab-sinai/pipelines_for_ChIP-seq_analysis
Pipelines for ChIP-seq analysis, such as peak calling, differential enrichment detection, and pausing index calculation for PolII.
shenlab-sinai/NGS-Data-Charmer
This repository hosts an automated NGS data analysis (RNA-seq and ChIP-seq) pipeline created using Snakemake.
shenlab-sinai/diffRepeats
Quantify repeat element enrichment with next-generation sequencing data
shenlab-sinai/Gene-Attributes
A shiny app that obtains the coordinates and description of an input gene list (Ensembl v90) using biomaRt package.
shenlab-sinai/miRNA_pipeline_for_miRanalyzer
A pipeline of miRNA by using miRanalyzer
shenlab-sinai/RRHO2
Optimized RRHO2
shenlab-sinai/software-best-practice
The best software engineering practices to develop bioinformatic programs
shenlab-sinai/geneoverlap-old
R package for testing and visualizing gene overlaps
shenlab-sinai/Isoseq_processing
shenlab-sinai/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.
shenlab-sinai/shen-bioinfo-R
A collection of R code to perform bioinformatics.