Shadow Regression
R package:
ShadowRegression_1.0.tar.gz
R code to try test data:
test.R
Expect 30-60 minutes of run time on test data provided, depending on
system.
Test data:
SRR037452.fastq.rcnts.gz
This is one of the MAQC samples. More information can be found from
the Short Read Archive.
PhiX genome in fasta format:
phix.fasta
History:
6/28/2013: Requires ShortRead version 1.18 or above. Earlier versions
may cause problems in function getReadCnts().
5/14/2013: Package rebuilt to be compatible with R 3.0.
5/11/2012: Package released.
Please cite:
Wang, X. V., Blades, N., Ding, J., Sultana, R., & Parmigiani,
G. (2012). Estimation of sequencing error rates in short reads. BMC
Bioinformatics, 13(1), 1-12.
Article can be found
at
http://www.biomedcentral.com/1471-2105/13/185/
Maintained by Victoria Wang (vwang at jimmy.harvard.edu).