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bioinformatics:scripts:nature [2014/05/05 16:45]
chrissch created
bioinformatics:scripts:nature [2015/10/15 22:37] (current)
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 +===== 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 ==== ==== Recruit2Cloud ====
 {{:​bioinformatics:​scripts:​recruit2cloud1-0-2.py.zip}}\\ {{:​bioinformatics:​scripts:​recruit2cloud1-0-2.py.zip}}\\
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 **Author:** Julio Cesar Ignacio-Espinoza\\ **Author:** Julio Cesar Ignacio-Espinoza\\
 **Last Revision:** Jan 2013\\ **Last Revision:** Jan 2013\\
-**Description:​** plotSmall\\ 
  
  
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 **Author:** Julio Cesar Ignacio-Espinoza\\ **Author:** Julio Cesar Ignacio-Espinoza\\
 **Last Revision:** Jan 2013\\ **Last Revision:** Jan 2013\\
-**Description:​** ​SizeandLocation\\+ 
 +==== 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.\\ 
 + 
 +==== matrix2PCA.m ==== 
 +{{:​bioinformatics:​scripts:​matrix2pca.m.zip}}\\ 
 +**Author:** Julio Cesar Ignacio-Espinoza\\ 
 +**Last Revision:** Dec 2013\\ 
 +**Description:​** Matlab list of commands, input is a m x n matrix where m is the number of observations and n is the number of variables measured.\\  
 + 
 +==== read2genome.pl ==== 
 +{{:​bioinformatics:​scripts:​read2genome.pl.zip}}\\ 
 +**Author:** Julio Cesar Ignacio-Espinoza\\ 
 +**Last Revision:** Dec 2013\\ 
 +**Description:​** The input files are a blastn file and a reference file. It aligns the best hits to the reference dataset, It outputs a per base frequency of nucleotides along the reference genome.\\ 
 + 
 +==== randomGenome.pl ==== 
 +{{:​bioinformatics:​scripts:​randomgenome.pl.zip}}\\ 
 +**Author:** Julio Cesar Ignacio-Espinoza\\ 
 +**Last Revision:** Dec 2013\\ 
 +**Description:​** The input is the output of read2genome.pl. It generates a set of random contigs based on their per base frequency.\\  
 + 
 +==== chopGenome.pl ==== 
 +{{:​bioinformatics:​scripts:​chopgenome.pl.zip}}\\ 
 +**Author:** Julio Cesar Ignacio-Espinoza\\ 
 +**Last Revision:** Dec 2013\\ 
 +**Description:​** The input is a fasta file, it outputs a multi fasta file where the original file has been cut.  
  
bioinformatics/scripts/nature.1399322725.txt.gz · Last modified: 2015/10/15 22:47 (external edit)
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