Bioinformatics Tools developed by our team

RSeQC

• RSeQC package provides many useful python modules to QC, analyze and visualize RNA-seq data.
• Reference: Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012 Aug 15;28(16):2184-5. doi: 10.1093/bioinformatics/bts356. Epub 2012 Jun 27. PMID: 22743226.

CPAT

• CPAT (Coding-Potential Assessment Tool) trained a logistic regression model from pure sequence features to distinguish noncoding RNAs from protein coding mRNAs.
• Webserver
• Reference: Wang L, Park HJ, Dasari S, Wang S, Kocher JP, Li W. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013 Apr 1;41(6):e74. doi: 10.1093/nar/gkt006. Epub 2013 Jan 17. PMID: 23335781; PMCID: PMC3616698.

CrossMap

• CrossMap is a program to liftover genome coordinates between different genome assemblies. It supports multiple file formats including BED, BAM/SAM/CRAM, VCF, Wiggle/BigWig, etc.
• Reference: Zhao H, Sun Z, Wang J, Huang H, Kocher JP, Wang L. CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics. 2014 Apr 1;30(7):1006-7. doi: 10.1093/bioinformatics/btt730. Epub 2013 Dec 18. PMID: 24351709; PMCID: PMC3967108.

MACE

• MACE (Model-based Analysis of ChIP-Exo) is a program dedicated to analyse ChIP-exo data.
• Reference: Wang L, Chen J, Wang C, Uusküla-Reimand L, Chen K, Medina-Rivera A, Young EJ, Zimmermann MT, Yan H, Sun Z, Zhang Y, Wu ST, Huang H, Wilson MD, Kocher JP, Li W. MACE: model based analysis of ChIP-exo. Nucleic Acids Res. 2014 Nov 10;42(20):e156. doi: 10.1093/nar/gku846. Epub 2014 Sep 23. PMID: 25249628; PMCID: PMC4227761.

Epidaurus

• Epidaurus is software to analyze and visualize different types of epigenomic data.
• Reference: Wang L, Huang H, Dougherty G, Zhao Y, Hossain A, Kocher JP. Epidaurus: aggregation and integration analysis of prostate cancer epigenome. Nucleic Acids Res. 2015 Jan;43(2):e7. doi: 10.1093/nar/gku1079. Epub 2014 Nov 5. PMID: 25378314; PMCID: PMC4333365.

PVAAS

• PVAAS is a program to identify single nucleotide variants that are associated with aberrant RNA splicing.
• Reference: Wang L, Nie JJ, Kocher JP. PVAAS: identify variants associated with aberrant splicing from RNA-seq. Bioinformatics. 2015 May 15;31(10):1668-70. doi: 10.1093/bioinformatics/btv001. Epub 2015 Jan 7. PMID: 25573917; PMCID: PMC4807355.

CircularLogo

• CircularLogo is an innovative web application that specifically designed to visualize and explore intra-motif dependencies. It is able to display intra-motif dependencies and reveal biomolecular structure effectively.
• Reference: Ye Z, Ma T, Kalmbach MT, Dasari S, Kocher JA, Wang L. CircularLogo: A lightweight web application to visualize intra-motif dependencies. BMC Bioinformatics. 2017 May 22;18(1):269. doi: 10.1186/s12859-017-1680-2. PMID: 28532394; PMCID: PMC5440937.

TIN

• TIN (Transcript Integrity Number) is an algorithm to measure RNA degradation at transcript level. It can improve differential gene expression analyses by reducing false positives and false negatives.
• Reference: Wang L, Nie J, Sicotte H, Li Y, Eckel-Passow JE, Dasari S, Vedell PT, Barman P, Wang L, Weinshiboum R, Jen J, Huang H, Kohli M, Kocher JP. Measure transcript integrity using RNA-seq data. BMC Bioinformatics. 2016 Feb 3;17:58. doi: 10.1186/s12859-016-0922-z. PMID: 26842848; PMCID: PMC4739097.

CpGtools

• CpGtools is a Python package to perform DNA methylation analysis.
• Reference: Wei T, Nie J, Larson NB, Ye Z, Eckel-Passow JE, Robertson KD, Kocher JA, Wang L. CpGtools: a python package for DNA methylation analysis. Bioinformatics. 2021 Jul 12;37(11):1598-1599. doi: 10.1093/bioinformatics/btz916. PMID: 31808791; PMCID: PMC8275978.

Spiker

• Spiker is a Python package to analzye Spike-In ChIP-seq data.
• Reference: Wu D, Wang L, Huang H. Protocol to apply spike-in ChIP-seq to capture massive histone acetylation in human cells. STAR Protoc. 2021 Jul 17;2(3):100681. doi: 10.1016/j.xpro.2021.100681. PMID: 34337446; PMCID: PMC8313745.

cobind

• Cobind is designed for quantitative analysis of the genomic overlaps.
• Reference: Ma T, Guo L, Yan H, and Wang L. Cobind: quantitative analysis of the genomic overlaps, Bioinformatics Advances, 2023;, vbad104, https://doi.org/10.1093/bioadv/vbad104