Pinned repositories

  1. ngsplot

    Quick mining and visualization of NGS data by integrating genomic databases

    R 107 46

  2. diffreps

    Differential analysis for ChIP-seq with biological replicates

    Perl 15 11

  3. region_analysis

    A python script used to annotate genomic intervals.

    Python 16 8

  4. chip-seq_preprocess

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

    Python 17 22

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

    Python 1 Updated Aug 16, 2018
  • A shiny app that obtains the coordinates and description of an input gene list (Ensembl v90) using biomaRt package.

    R 1 Updated Jun 22, 2018
  • 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 Updated Mar 27, 2018
  • Quick mining and visualization of NGS data by integrating genomic databases

    R 107 46 GPL-2.0 Updated Jul 24, 2017
  • A Scalable Pipeline for RNA‬‬‬-seq Ana‬‬lysis

    Python 7 6 Updated May 4, 2017
  • A preprocessing pipeline for ChIP-seq, including alignment, quality control, and visualization.

    Python 17 22 GPL-2.0 Updated Apr 24, 2017
  • Differential analysis for ChIP-seq with biological replicates

    Perl 15 11 GPL-2.0 Updated Nov 4, 2016
  • Quantify repeat element enrichment with next-generation sequencing data

    Perl 1 GPL-3.0 Updated Aug 26, 2016
  • R package for testing and visualizing gene list overlaps

    R 2 1 Updated Aug 22, 2016
  • R package for testing and visualizing gene overlaps

    R 1 Updated Aug 22, 2016
  • A python script used to annotate genomic intervals.

    Python 16 8 GPL-3.0 Updated Aug 19, 2016
  • Genome databases generation pipeline for ngs.plot and region_analysis.

    Shell 7 4 GPL-2.0 Updated Sep 8, 2015
  • A pipeline of miRNA by using miRanalyzer

    Python 4 LGPL-2.1 Updated Jul 17, 2014
  • Pipelines for ChIP-seq analysis, such as peak calling, differential enrichment detection, and pausing index calculation for PolII.

    R 4 9 LGPL-2.1 Updated Jul 14, 2014
  • Shenlab's unofficial (but most updated) website

    CSS Updated Apr 23, 2014
  • The best software engineering practices to develop bioinformatic programs

    1 2 Updated Jan 24, 2014
  • A collection of R code to perform bioinformatics.

    R 2 GPL-3.0 Updated Dec 19, 2013