Citations

[grabear]

Some of the citations have been accumulated in the old documentation file: https://github.com/vallenderlab/stress-microbiome-analysis/blob/rag-analysis2/Archive/Documentation/Stress_Microbiome_Project.Rmd

Pipeline Specifications and Citations

R and R packages

> R.version
  platform       x86_64-w64-mingw32          
arch           x86_64                      
os             mingw32                     
system         x86_64, mingw32             
status                                     
major          3                           
minor          4.3                         
year           2017                        
month          11                          
day            30                          
svn rev        73796                       
language       R                           
version.string R version 3.4.3 (2017-11-30)
nickname       Kite-Eating Tree

# There are more packages to add I think
> get_default_parameters(func_names = "packages")
$required_cran_packages
 [1] "devtools"    "ggplot2"     "plotly"      "dplyr"       "rstudioapi"  "diptest"     "phytools"   
 [8] "taxa"        "modes"       "metacoder"   "gridExtra"   "lme4"        "vegan"       "tidyr"      
[15] "VennDiagram" "extrafont"  

$required_bioconductor_packages
[1] "phyloseq"   "ggtree"     "biomformat" "microbiome" "PathoStat" 

$required_github_packages
[1] "MadsAlbertsen/ampvis2"

Nephele Pipeline

• Nephele 1.8 (June 30, 2017)

  • QIIME 1.9.1
  • UCHIME 4.2
  • Mothur v.1.39.5
  • SORTMERNA v 2.0
  • SILVA database release 128

• Citations

  • Citing Nephele

  In articles and other publications, please cite Nephele as follows:

  Office of Cyber Infrastructure and Computational Biology (OCICB), National Institute of Allergy and Infectious Diseases (NIAID). Nephele. http://nephele.niaid.nih.gov (2016)

  Alternatively, use the following acknowledgement:

  "This study used the Nephele platform from the National Institute of Allergy and Infectious Diseases >(NIAID) Office of Cyber Infrastructure and Computational Biology (OCICB) in Bethesda, MD."

  Please also report the publication of articles which made use of Nephele by providing the reference in an >email to the Nephele Project Team.

  • Citing Qiime

  For QIIME or mothur (16s or 18s) please cite both of the following along with Nephele: mothur Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, >Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF. Introducing mothur: Open-source, >platform-independent, community-supported software for describing and comparing microbial communities. >Appl Environ Microbiol. 2009;75(23):7537-41.

  QIIME Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Gonzalez Pena A, >Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, >Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld >J, Knight R. QIIME allows analysis of high-throughput community sequencing data. Nature Methods. >2010;7(5):335-336., qiime.org

  • Citing SORTMERNA

  Kopylova, E., Noe L. and Touzet, H., SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data, Bioinformatics (2012) 28(24)

  • Citing SIVLA 128

  Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J, Glöckner FO (2013) The SILVA >ribosomal RNA gene database project: improved data processing and web-based tools. Opens external link in >new windowNucl. Acids Res. 41 (D1): D590-D596.

  Yilmaz P, Parfrey LW, Yarza P, Gerken J, Pruesse E, Quast C, Schweer T, Peplies J, Ludwig W, Glöckner FO >(2014) The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks. Opens external link in >new windowNucl. Acids Res. 42:D643-D648

  If you use SINA please cite:

  Pruesse, E, Peplies, J and Glöckner, FO (2012) SINA: accurate high-throughput multiple sequence alignment >of ribosomal RNA genes. Opens external link in new windowBioinformatics, 28, 1823-1829

  • Citing UCHIME

  Edgar,RC, Haas,BJ, Clemente,JC, Quince,C, Knight,R. 2011. UCHIME improves sensitivity and speed of >chimera detection. Bioinformatics btr381.

  Edgar RC. 2010. Search and clustering orders of magnitude faster than BLAST. Bioinformatics >26(19):2460-2461.

[sdhutchins]

Are we using something from PathoStat? I think the biggest thing I need to do is make sure I'm using what I'm importing.

[grabear]

I haven't used it, but I'm not really keeping up with it well. I haven't gone through and sorted what I am and I'm not using. ggtree for instance may not be used...

[grabear]

I used these papers to make many of my decisions:

• https://bioconductor.org/help/course-materials/2017/BioC2017/Day1/Workshops/Microbiome/MicrobiomeWorkflowII.html

• https://f1000research.com/articles/5-1492/v2

• https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-3501-4

[sdhutchins]

Use the grateful package to cite R packages.