Monthly Archives: June 2015

R-3.2.0

Maths @en

General Information

R is ‘GNU S’, a freely available language and environment for statistical computing and graphics which provides a wide variety of statistical and graphical techniques: linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, etc. Please consult the R project homepage for further information.

Installed Packages

lavaan, mnormt, psych, Rcmdr, abind, e1071, xlsx, biocLite(),FactoMineR

Please ask if you need any more.

How to use it

To use R-3.2  execute:

/software/R-3.2.0/bin/R CMD BATCH input.R

More Information:

http://cran.r-project.org/

USEARCH

Genetics, Scientific Software

General information

USEARCH is a unique sequence analysis tool that offers search and clustering algorithms that are often orders of magnitude faster than BLAST. We have the free 32 bits version that can not be distributed to third parties and has a 4 GB of RAM limitation.

How to use

To use USEARCH execute

/software/bin/usearch

for example

/software/bin/usearch -cluster_otus data.fa -otus otus.fa -uparseout out.up -relabel OTU_ -sizein -sizeout

USEARCH is only available in the xeon20 type nodes.

QIIME

USEARCH can be use under [intlink id=”7758″ type=”post”]QIIME[/intlink].

More information

USEARCH home page.

[intlink id=”7686″ type=”post”]QIIME[/intlink].