Aaditya V. Rangan

Courant Institute of Mathematical Sciences, New York University,

251 Mercer Street, New York, NY 10012.

Phone: (212) 998-3303, email: rangan (at) cims (dot) nyu (dot) edu

webpage: http://www.cims.nyu.edu/~rangan/

Office Hours Fall 2015: Thursday 1:30pm-3:25pm

Room: 1123 WWH

Research Interests: Applications of numerical-analysis and scientific-computing to the biological sciences.

CV (last updated 02/15/18)

List of publications (last updated 02/15/18)

Recently I've been developing a 'loop-counting' algorithm for biclustering gene-expression data. I believe the results are rather promising.

Link to paper (last updated 05/14/18)

Here is a tutorial which presents an example of this algorithm applied to a standard data set (last updated 07/22/15):

(tutorial in pdf),(tutorial in pptx).

A much more detailed explanation of this loop-counting algorithm is given in:

(Preprint).

(Supplementary Material).

The files associated with the tutorial above are bundled into the following archives:

(level-0): This "level-0" archive contains all the basic matlab files needed to generate the output shown in the presentation. Each of the matlab files is documented internally (e.g., you can run '>> help tutorial_w1;' to see what the file tutorial_w1.m does). Note that this archive does not include the output itself. Thus, some runtime will be necessary if you want to bicluster everything yourself.

(level-1): Just like the "level-0" archive, this "level-1" archive contains the matlab files needed to generate the output shown in the presentation. In addition, the "level-1" archive also contains the output for the original data. This archive does not include all the label-shuffled trials used to generate p-values for the original data. Thus, some runtime will be necessary if you want to generate p-values yourself.

(level-2): As above, this "level-2" archive contains all files needed to generate the output. In addition, the "level-2" archive also contains all the output for both the original data and the label-shuffled permutations. If you download this archive you should be able to immediately generate the summary plots by running 'tutorial_summarize' or 'tutorial_plot'.

A significantly more efficient implementation of this algorithm (written in C) is available at:

lakcluster_ver18.tar.gz (last updated 09/26/18)

lakcluster_ver18 on github

This implementation also includes several subroutines which perform binary vector-vector, matrix-vector and matrix-matrix operations.

251 Mercer Street, New York, NY 10012.

Phone: (212) 998-3303, email: rangan (at) cims (dot) nyu (dot) edu

webpage: http://www.cims.nyu.edu/~rangan/

Office Hours Fall 2015: Thursday 1:30pm-3:25pm

Room: 1123 WWH

Research Interests: Applications of numerical-analysis and scientific-computing to the biological sciences.

CV (last updated 02/15/18)

List of publications (last updated 02/15/18)

Recently I've been developing a 'loop-counting' algorithm for biclustering gene-expression data. I believe the results are rather promising.

Link to paper (last updated 05/14/18)

Here is a tutorial which presents an example of this algorithm applied to a standard data set (last updated 07/22/15):

(tutorial in pdf),(tutorial in pptx).

A much more detailed explanation of this loop-counting algorithm is given in:

(Preprint).

(Supplementary Material).

The files associated with the tutorial above are bundled into the following archives:

(level-0): This "level-0" archive contains all the basic matlab files needed to generate the output shown in the presentation. Each of the matlab files is documented internally (e.g., you can run '>> help tutorial_w1;' to see what the file tutorial_w1.m does). Note that this archive does not include the output itself. Thus, some runtime will be necessary if you want to bicluster everything yourself.

(level-1): Just like the "level-0" archive, this "level-1" archive contains the matlab files needed to generate the output shown in the presentation. In addition, the "level-1" archive also contains the output for the original data. This archive does not include all the label-shuffled trials used to generate p-values for the original data. Thus, some runtime will be necessary if you want to generate p-values yourself.

(level-2): As above, this "level-2" archive contains all files needed to generate the output. In addition, the "level-2" archive also contains all the output for both the original data and the label-shuffled permutations. If you download this archive you should be able to immediately generate the summary plots by running 'tutorial_summarize' or 'tutorial_plot'.

A significantly more efficient implementation of this algorithm (written in C) is available at:

lakcluster_ver18.tar.gz (last updated 09/26/18)

lakcluster_ver18 on github

This implementation also includes several subroutines which perform binary vector-vector, matrix-vector and matrix-matrix operations.