Table 1 Algorithms and code sources used in MutSpec

Annovar^a

June 2015

X

-

-

-

[17]

Statistics::R^a

0.33

-

X

-

-

http://search.cpan.org/~gmpassos/Statistics-R-0.02/lib/Statistics/R.pm#AUTHOR

Spreadsheet::

WriteExcel^a

2.40

-

X

-

-

http://search.cpan.org/~jmcnamara/Spreadsheet-WriteExcel-2.40/lib/Spreadsheet/WriteExcel.pm

ggplot2

1.0.1

-

X

X

X

http://ggplot2.org/

gplots

2.17.0

-

X

-

-

http://cran.r-project.org/web/packages/gplots/gplots.pdf

gtable

0.1.2

-

X

-

-

http://cran.r-project.org/web/packages/gtable/gtable.pdf

reshape

1.4.1

-

X

X

X

http://cran.r-project.org/web/packages/reshape/reshape.pdf

scales

0.2.5

-

X

X

-

http://cran.r-project.org/web/packages/scales/scales.pdf

gridExtra

0.9.1

-

X

X

-

http://cran.r-project.org/web/packages/gridExtra/gridExtra.pdf

NMF

0.20.6

-

X

X

-

[18]

getopt

1.20.0

-

-

X

-

http://cran.r-project.org/web/packages/getopt/getopt.pdf

lsa

0.73.1

-

-

-

X

http://cran.r-project.org/web/packages/lsa/lsa.pdf