Tools I have developed

IPGWAS: Integrated Pipeline for Genome-Wide Association Studies

IPGWAS was developed to facilitate the identification of the rational thresholds in QC of GWAS datasets, association analysis, Manhattan plot, quantile-quantile (QQ) plot, and format conversion for genetic analyses, such as meta-analysis, genotype phasing, and imputation. IPGWAS is a multiplatform application written in Perl with a graphical user interface (GUI).

IPGWAS is available at sourceforge and GitHub.

Citation: Fan YH, Song YQ.IPGWAS: an integrated pipeline for rational quality control and association analysis of genome-wide genetic studies. Biochem Biophys Res Commun. 2012 Jun 8;422(3):363-8. PubMed.

FinCal: Time Value of Money, time series analysis and Computational Finance

FinCal is a R Package for time value of money calculation, time series analysis and computational finance. Currently, the fuctions are as following:

  • Financial calculator for time value money: PV, FV, N, PMT, I/Y
  • NPV, IRR
  • Methods for downloading historical stock prices from Yahoo finance and Google finance
  • Technical analysis
  • Cost of goods sold and ending inventory under three methods (FIFO,LIFO,Weighted average)

More details and examples of using FinCal is available here

FinCal is available at CRAN and GitHub

PubMedWordcloud: PubMed Word Clouds

PubMedWordcloud is a R Package for creating a word cloud using the abstract of publications from PubMed. PubMedWordcloud makes it easy to created a word cloud using the abstracts of your publications to represent a visual description of your work.

More details and examples of using PubMedWordcloud is available here

PubMedWordcloud is available at CRAN and GitHub

Chi-Square Calculator

A Java tool computes cumulative probabilities, based on the chi-square statistic.

  • 2 x 2 contingency table.
  • 2 x 3 contingency table.
  • chi-square statistic and degrees of freedom

ChiSquareCalculator is available at GitHub