Skip to content

@shenlab-sinai Shen Lab at Mount Sinai

Change the repository type filter

All

    Repositories list

    19 repositories

    • DeepRegFinder

      Public
      DeepRegFinder is a deep learning based program used to identify DNA regulatory elements using ChIP-seq
      Python
      •
      Other
      •2•9•0•2•Updated Mar 28, 2024Mar 28, 2024

    • NGS-Data-Charmer

      Public
      This repository hosts an automated NGS data analysis (RNA-seq and ChIP-seq) pipeline created using Snakemake.
      Python
      •3•4•1•1•Updated Jan 24, 2024Jan 24, 2024

    • ngsplot

      Public
      Quick mining and visualization of NGS data by integrating genomic databases
      R
      •
      Other
      •65•261•54•1•Updated May 5, 2023May 5, 2023

    • Gene-Attributes

      Public
      A shiny app that obtains the coordinates and description of an input gene list (Ensembl v90) using biomaRt package.
      R
      •3•1•0•0•Updated Mar 23, 2023Mar 23, 2023

    • diffreps

      Public
      Differential analysis for ChIP-seq with biological replicates
      Perl
      •
      Other
      •16•35•8•1•Updated Jan 5, 2022Jan 5, 2022

    • RRHO2

      Public
      Optimized RRHO2
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Jun 18, 2020Jun 18, 2020

    • Isoseq_processing

      Public
      Python
      •0•0•0•0•Updated Jun 4, 2020Jun 4, 2020

    • region_analysis

      Public
      A python script used to annotate genomic intervals.
      Python
      •
      GNU General Public License v3.0
      •10•18•7•1•Updated May 29, 2020May 29, 2020

    • RRHO_Modified.R

      Public
      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.
      R
      •1•0•1•0•Updated Jan 14, 2020Jan 14, 2020

    • SPEctRA

      Public
      A Scalable Pipeline for RNA‬‬‬-seq Ana‬‬lysis
      Python
      •7•9•14•0•Updated May 4, 2017May 4, 2017

    • chip-seq_preprocess

      Public
      A preprocessing pipeline for ChIP-seq, including alignment, quality control, and visualization.
      Python
      •
      GNU General Public License v2.0
      •31•27•1•0•Updated Apr 24, 2017Apr 24, 2017

    • diffRepeats

      Public
      Quantify repeat element enrichment with next-generation sequencing data
      Perl
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Aug 26, 2016Aug 26, 2016

    • GeneOverlap

      Public
      R package for testing and visualizing gene list overlaps
      R
      •2•18•4•0•Updated Aug 22, 2016Aug 22, 2016

    • geneoverlap-old

      Public
      R package for testing and visualizing gene overlaps
      R
      •1•0•1•0•Updated Aug 22, 2016Aug 22, 2016

    • ngsplotdb

      Public
      Genome databases generation pipeline for ngs.plot and region_analysis.
      Shell
      •
      GNU General Public License v2.0
      •5•16•1•0•Updated Sep 8, 2015Sep 8, 2015

    • miRNA_pipeline_for_miRanalyzer

      Public
      A pipeline of miRNA by using miRanalyzer
      Python
      •
      GNU Lesser General Public License v2.1
      •6•1•1•0•Updated Jul 17, 2014Jul 17, 2014

    • pipelines_for_ChIP-seq_analysis

      Public
      Pipelines for ChIP-seq analysis, such as peak calling, differential enrichment detection, and pausing index calculation for PolII.
      R
      •
      GNU Lesser General Public License v2.1
      •13•8•1•1•Updated Jul 14, 2014Jul 14, 2014

    • software-best-practice

      Public
      The best software engineering practices to develop bioinformatic programs
      3•1•0•0•Updated Jan 25, 2014Jan 25, 2014

    • shen-bioinfo-R

      Public
      A collection of R code to perform bioinformatics.
      R
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Dec 19, 2013Dec 19, 2013