Announcement (2016-10-01):
To fulfill the requirements of different Axiom SNP arrays and laboratories, we can provide customized reference databases of ALICE for you. If you have the need, please email Dr. Hsin-Chou Yang (hsinchou@stat.sinica.edu.tw). |
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Introduction: | ||||||||||||||||||||||||||||||||||||||
ALICE
(AF/LOH/LCSH/AI/CNV/CNA Enterprise) is user-friendly software for an
integrated analysis of allele frequency (AF), allelic imbalance (AI),
loss of heterozygosity (LOH), long contiguous stretch of homozygosity
(LCSH), and copy number variation or alteration (CNV/CNA) on the basis
of SNP probe hybridization intensities and genotypes. The software,
user manual, library files for APT, annotation files, test examples,
and reference databases can be downloaded below. |
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Reference (* correspondence author): |
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Mei-Chu Huang, Tze-Po Tsuang, Chien-Hsiun Chen, Jer-Yuarn Wu, Yuan-Tsong Chen, Ling-Hui Li*, and Hsin-Chou Yang* (2015) An Integrated Analysis Tool for Analyzing Hybridization Intensities and Genotypes Using New-Generation Population-Optimized Human Arrays. BMC Genomics 17:266. (http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2478-8) |
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Contact: |
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Please kindly acknowledge if you have downloaded ALICE. We will inform you the update of ALICE. Any questions, comments and suggestions on ALICE are welcome. Please send your feedback to hsinchou@stat.sinica.edu.tw. |
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Download software & user manual: |
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* We provide a default example in the ALICE software. Therefore, the file is somewhat large! |
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Download library files for Affymetrix Power Tools (APT): |
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Download annotation files: |
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For Affymetrix:
For Illumina: |
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Download examples: |
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Download database: |
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Popultaion | Platform | Input data format | Sample size |
Parameter (w, nc) |
Database index (Description) | |||||||
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | |||||
Han Chinese in Taiwan
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Affymetrix 100K |
GTC-exported text file |
367 | (11 , 2) | ||||||||
(51 , 3) | ||||||||||||
Affymetrix 500K |
GTC-exported text file |
448 | (11 , 2) | |||||||||
(51 , 3) | ||||||||||||
Affymetrix Array 6.0 |
Probe results file (*.CEL) |
1,013 | (11 , 2) | |||||||||
(51 , 3) | ||||||||||||
GTC-exported text file |
1,013 | (11 , 2) | ||||||||||
(51 , 3) | ||||||||||||
Affymetrix Axiom CHB |
Probe results file (*.CEL) |
1,666 | (11 , 2) | |||||||||
(51 , 3) | ||||||||||||
GTC-exported text file |
1,666 | (11 , 2) | ||||||||||
(51 , 3) | ||||||||||||
Illumina |
BS-exported text file |
854 | (11 , 2) | |||||||||
(51 , 3) |
Popultaion | Platform | Input data format | Sample size |
Parameter (w, nc) |
Database index (Description) | |||||||
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | |||||
Asian (CHB + JPT)
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Affymetrix Array 6.0 |
Probe results file (*.CEL) |
90 | (11 , 2) | |||||||||
(51 , 3) |
Popultaion | Platform | Input data format | Sample size |
Parameter (w, nc) |
Database index (Description) | |||||||
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | |||||
CEU
|
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Affymetrix Array 6.0 |
Probe results file (*.CEL) |
60 | (11 , 2) | |||||||||
(51 , 3) |
Popultaion | Platform | Input data format | Sample size |
Parameter (w, nc) |
Database index (Description) | |||||||
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | |||||
CHB
|
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Affymetrix Array 6.0 |
Probe results file (*.CEL) |
45 | (11 , 2) | |||||||||
(51 , 3) |
Popultaion | Platform | Input data format | Sample size |
Parameter (w, nc) |
Database index (Description) | |||||||
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | |||||
JPT
|
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Affymetrix Array 6.0 |
Probe results file (*.CEL) |
45 | (11 , 2) | |||||||||
(51 , 3) |
Popultaion | Platform | Input data format | Sample size |
Parameter (w, nc) |
Database index (Description) | |||||||
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | |||||
YRI
|
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Affymetrix Array 6.0 |
Probe results file (*.CEL) |
60 | (11 , 2) | |||||||||
(51 , 3) |
Popultaion | Platform | Input data format | Sample size |
Parameter (w, nc) |
Database index (Description) | |||||||
1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | |||||
Combined (CEU + CHB + JPT + YRI)
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Affymetrix Array 6.0 |
Probe results file (*.CEL) |
210 | (11 , 2) | |||||||||
(51 , 3) |