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Identification of a functional downstream core promoter element in human promoters using an Expectation-Maximization algorithm

License: GNU General Public License v3.0

R 95.59% HTML 2.62% Shell 1.29% Perl 0.51%
publication publication-code publication-data expectation-maximization-algorithm dna-motif motif-discovery

humandpe's Introduction

R scripts and data collections to generate the analysis and figures
published in:

* Computational identification and experimental characterization 
  of preferred downstream positions in human core promoters  

Please refer to the README files in eash subdirectory for a detailed
description of the scripts and data.

humandpe's People

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humandpe's Issues

Issues in fig2.R (identified in SIB days reproducibility hackathon)

  1. Class checks in seqLogo2 not working:

`seqLogo2(pwm,xfontsize=6, yfontsize=6, title="Class 1 (Inr+DPE), 37.2%")
Error in if (class(pwm) == "pwm") { : the condition has length > 1

class(pwm)
[1] "matrix" "array"`

As a work around: comment out lines 3-13 in seqLogo2_fig2.R

  1. Wrong input files linked for human plot

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