Differences

This shows you the differences between two versions of the page.

Link to this comparison view

bioinformatics:scripts:nature [2014/05/05 17:53]
chrissch
bioinformatics:scripts:nature [2015/10/15 22:37]
Line 1: Line 1:
-===== Viral tagging reveals discrete populations in Synechococcus viral genome sequence space ===== 
-**Associate manuscript for all scripts on this page:** Deng, L., Ignacio-Espinoza,​ J.C., Gregory, A., Poulos, B.T., Weitz, J.S., Hugenholtz, P., Sullivan, M.B. (accepted). Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature. 
  
- 
-==== recruitment ==== 
-{{:​bioinformatics:​scripts:​recruitment.txt.zip}}\\ 
-**Author:** Julio Cesar Ignacio-Espinoza\\ 
-**Last Revision:** July 2011\\ 
- 
-==== Recruit2Cloud ==== 
-{{:​bioinformatics:​scripts:​recruit2cloud1-0-2.py.zip}}\\ 
-**Author:** Julio Cesar Ignacio-Espinoza\\ 
-**Last Revision:** Sep 2012\\ 
-**Description:​** Recruit2cloud01.pl takes a series of genome reads, a reference genome, and a blastn of the reference genome (in that order) to generate a COV file. Each line in the COV file corresponds to all the bases found in that position after aligning the reads to the blastn output with muscle. The first-order option and file descriptor and option represent the file with the return-delimited list of genome reads. The second-order option and file descriptor and option represents the file with the reference genome. The third-order option and file descriptor and option represents the file with the blastn output of the reference genome.\\ 
- 
-==== plotSmall ==== 
-{{:​bioinformatics:​scripts:​plotsmall.pl.zip}}\\ 
-**Author:** Julio Cesar Ignacio-Espinoza\\ 
-**Last Revision:** Jan 2013\\ 
- 
- 
-==== SizeandLocation ==== 
-{{:​bioinformatics:​scripts:​sizeandlocation.pl.zip}}\\ 
-**Author:** Julio Cesar Ignacio-Espinoza\\ 
-**Last Revision:** Jan 2013\\ 
- 
-==== rarefaction ==== 
-{{:​bioinformatics:​scripts:​rarefaction.pl.zip}}\\ 
-**Author:** Julio Cesar Ignacio-Espinoza\\ 
-**Last Revision:** Nov 2013\\ 
-**Description:​** Generates a rarefaction curve from resampling a tabulated list of reads and its assigned protein cluster.\\ 
- 
-==== dunns ==== 
-{{:​bioinformatics:​scripts:​dunns.m.zip}}\\ 
-**Author:** Julio Cesar Ignacio-Espinoza\\ 
-**Last Revision:** Nov 2013\\ 
-**Description:​** Calculates Dunn's index as a way to asses the compactness and separation of clusters.\\ 
- 
-==== dunnRdm ==== 
-{{:​bioinformatics:​scripts:​dunnRdm.m.zip}}\\ 
-**Author:** Julio Cesar Ignacio-Espinoza\\ 
-**Last Revision:** Nov 2013\\ 
-**Description:​** Generates a random distribution of Dunn's index values from the data to evaluate the observed Dunn's index. Then the effect size (z-score) serves as a direct form of evaluation of the observed value. \\ 
- 
-==== Acc ==== 
-{{:​bioinformatics:​scripts:​Acc.m.zip}}\\ 
-**Author:** Julio Cesar Ignacio-Espinoza\\ 
-**Last Revision:** Nov 2013\\ 
-**Description:​** Calculates the accuracy of assignation of clusters. Data points are assigned to the closest cluster centroid. Then, accuracy of assignation Q, becomes the ratio of accurate assignations to the total number of observations.\\ 
- 
-==== AccRdm ==== 
-{{:​bioinformatics:​scripts:​AccRdm.m.zip}}\\ 
-**Author:** Julio Cesar Ignacio-Espinoza\\ 
-**Last Revision:** Nov 2013\\ 
-**Description:​** Generates a random distribution of values of Q. The effect ​ size can be obtained by comparing this distribution to the observed values of Q.\\ 
bioinformatics/scripts/nature.txt ยท Last modified: 2015/10/15 22:37 (external edit)
CC Attribution-Noncommercial-Share Alike 3.0 Unported
www.chimeric.de Valid CSS Driven by DokuWiki do yourself a favour and use a real browser - get firefox!! Recent changes RSS feed Valid XHTML 1.0