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TileMap

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A computational tool to make tiling array analysis and to detect genomic loci that show hybridization patterns of interest. TileMap includes functions to (i) compute probe-level test-statistics according to the transcriptional or protein binding patterns specified by users; (ii) filter local repeats; and (iii) infer if a region is of interest or not by applying hidden markov model or moving window average (MA). Compared with previous tools, TileMap provides a flexible way to study tiling array hybridizations under multiple experimental conditions.

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TileMap classification

TileMap specifications

Software type:
Package/Module
Restrictions to use:
None
Output format:
REG, BED, SUM, TXT
Computer skills:
Advanced
Stability:
Stable
Interface:
Command line interface
Output data:
The output of tilemap includes files which provide summary statistics for each probe, a file which reports regions of interest, and a file which sorts the reported regions from high to low significance level. Files can be uploaded directly to UCSC genome browser to visualize the reported regions.
Operating system:
Unix/Linux, Mac OS, Windows
Version:
2.0
Maintained:
Yes

TileMap distribution

versioning

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No versioning.

TileMap support

Documentation

Maintainer

  • Wing Hung Wong <>

Credits

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Publications

Institution(s)

Department of Statistics, Harvard University Cambridge, MA, USA; Department of Statistics, Stanford University Stanford, CA, USA

Funding source(s)

The work was partially supported by NIH grant GM-067250.

Link to literature

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.