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Hongbo Liu - Development of bioinformatics tools for epigenetics study
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Hongbo Liu

Development of bioinformatics tools for epigenetics study
Search Institute • Minneapolis • United States of America

Skills and expertise

Fields of interest
  • ChIP-seq analysis
  • BS-seq analysis
  • DNA methylation array analysis
Languages
  • Chinese
  • English
Programming languages
  • C
  • Java
  • MATLAB
  • Perl
  • Python
  • R
  • Shell (Bash)

Reviews and Discussions

LATEST REVIEWS

SMART 2017-08-08, 17:03:57
SMART2 is a newly developed tool for deep analysis of DNA methylation data detected by bisulfite sequencing platforms. This tool is focused on three main functions including de novo identification of…

LATEST DISCUSSIONS

Open
QDMR 2017-08-08, 17:50:57
0 comments
http://fame.edbc.org/qdmr/
Open
SMART 2017-08-08, 17:05:00
0 comments
http://fame.edbc.org/smart/

TOOLS MAINTAINED

SMART

Desktop

SMART / Specific Methylation Analysis and Report Tool

(1) 1 discussion(s)
Detects the cell type-specific methylation marks by integrating multiple methylomes from human cell lines and tissues. SMART is an entropy-based framework focused on integrating of a large number of…

QDMR

Desktop

QDMR / Quantitative Differentially Methylated Region

(0) 1 discussion(s)
Allows users to quantify methylation difference and identify differentially methylated regions (DMRs) across multiple samples. QDMR is a quantitative approach genome-wide quantitative comparisons of…

Fields of interest

ChIP-seq analysis
Simplifies the execution of existing short read aligners (SRA) on…
Aligns raw reads directly against redundant databases. KMA is an alignment…
Permits to reconstruct transcriptional regulatory networks. TReNA uses gene…
BS-seq analysis
Serves as a fully automatic analysis of protein family conservation within a…
Allows users to process targeted enriched Illumina sequences from raw reads to…
Compresses coordinate sorted aligned SAM, BAM or CRAM files. Crumble is a…
DNA methylation array analysis
Consists of a genomic context explorer. GeneSpy is a program that aims to…
Enables users to analyze pathways based on the variability of the expression of…
Normalizes measurement of long gene expression (LGE) within RNA-seq and…