Downloads

Below are a list of programs and data files available from our lab.

 

AGEseq: Analysis of Genome Editing by Sequencing

Perl Script: AGEseq.zip

ReadMe file: AGEseq_Readme.docx

Blat for Windows XP, Vista, 7: blat_windows.zip

* This version will not work on Windows 10

Blat for Windows 10: blat_windows10.zip

* This version works on Windows 10 only.

Note: Only a small number of reads is provided in the test data. 

A complete set of data from one transgenic line is available here: 4CL1-61_S11.zip

 

SLIM: A Sliding Linear Model for Estimating the Proportion of True Null Hypotheses in Datasets With Dependence Structures.

dl.php.rar 

Citation: Wang H-Q, Tuominen LK, Tsai C-J (2011) Bioinformatics 27:225-231.

 

CorSig: A General Framework for Estimating Statistical Significance of Correlation and Its Application to Gene Co-expression Analysis.

54-corsig.rar 

Citation: Wang H-Q and Tsai C-J (2013) PLoS One 8(10): e77429.

 

Populus microarray annotation:

Affymetrix Poplar Chip annotation (against JGI release v2.2 or v3.0)

Citation: Tsai C-J, Ranjan P, DiFazio SP, Tuskan GA, Johnson V (2011) Poplar genome microarrays. In: Joshi CP, DiFazio SP and Kole C (eds), Genetics, Genomics and Breeding of Poplars. Science Publishers, Enfield, NH. pp. 112-127.

Agilent v1 Poplar Array annotation (against JGI release v2.2 or v3.0)

Citation: Tsai C-J, Ranjan P, DiFazio SP, Tuskan GA, Johnson V (2011) Poplar genome microarrays. In: Joshi CP, DiFazio SP and Kole C (eds), Genetics, Genomics and Breeding of Poplars. Science Publishers, Enfield, NH. pp. 112-127.

Agilent v1 Poplar Array annotation (against JGI release v2.2 or v3.0)

Citation: Xue L-J, Guo W, Yuan Y, Anino EO, Nyamdari B, Wilson MC, Frost CJ, Chen H-Y, Babst BA, Harding SA, Tsai C-J (2013) Plant Cell 25: 2714-2730.

 

Extraction of Promoter sequences from the genome:

The perl scripts and a readme file: sut_promoter.zip

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