Informática Aplicada a la Investigación Rotating Header Image

junio, 2015:

R-3.2.0

Informazio Orokorra

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.

Instalatutako paketeak

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

Besterenbat behar izanez gero, ezka iezaguzu.

Nola Erabili

R-3.2 exekutatzeko erabili:

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

Informazio Gehiago

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

R-3.2.0

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/

R-3.2

Información general

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.

Paquetes Instalados

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

Si se requiere alguno más, por favor, haznoslo saber.

Cómo usar

Para usar R-3.2  ejecutar:

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

Más información

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

USEARCH

Informazio orokorra

USEARCH is a unique sequence analysis tool that offers search and clustering algorithms that are often orders of magnitude faster than BLAST. Tenemos la versión de 32 bits que es gratuita, pero no distribuible a terceros. Tiene la limitación de 4 GB de RAM como máximo.

Cómo usar

USEARCH erabiltzeko erabili ondorengo komandoa

/software/bin/usearch

adibidez

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

Momentuz USEARCH xeon20 etiketa duten nodoetan dago eskuragarri

QIIME

USEARCH QIIME-pean erabili daiteke

Informazio gehiago

USEARCH home page.

QIIME.

USEARCH

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 QIIME.

More information

USEARCH home page.

QIIME.

QIIME

Información general

QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.

Cómo ejecutar

Para enviar trabajos de QIIME ejecutar el comando

send_qiime

y responder a las preguntas que nos realice.

USEARCH

QIIME puede usar el paquete USEARCH.

Más información

QIIME home page.

USEARCH.

 

 

USEARCH

Información general

USEARCH is a unique sequence analysis tool  that offers search and clustering algorithms that are often orders of magnitude faster than BLAST. Tenemos la versión de 32 bits que es gratuita, pero no distribuible a terceros y tiene la limitación de 4 GB de RAM como máximo.

Cómo usar

Para ejecutar USEARCH ejecutar en los scripts el comando

/software/bin/usearch

por ejemplo

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

Por el momento USEARCH solo está disponible en los nodos con etiqueta xeon20.

QIIME

USEARCH puede ser empleado bajo QIIME.

Más información

USEARCH home page.

QIIME.