Pecinka Lab:Resources: Difference between revisions

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[http://signal.salk.edu/ SALK SIGnAL]. Bunch of resources for Arabidopsis work, e.g. [http://signal.salk.edu/cgi-bin/tdnaexpress T-DNA orientation finder], [http://neomorph.salk.edu/epigenome/epigenome.html 'SALK Epigenome'] etc.   
[http://signal.salk.edu/ SALK SIGnAL]. Bunch of resources for Arabidopsis work, e.g. [http://signal.salk.edu/cgi-bin/tdnaexpress T-DNA orientation finder], [http://neomorph.salk.edu/epigenome/epigenome.html 'SALK Epigenome'] etc.   


[http://www.1001genomes.org/ 1001 GENOMES]. Great source of data for natural variation analysis. SNP data of individual accessions can be viewed also on the [http://signal.salk.edu/atg1001/3.0/gebrowser.php SALK 1001 GENOMES BROWSER].
[http://www.1001genomes.org/ 1001 GENOMES], [http://signal.salk.edu/atg1001/3.0/gebrowser.php SALK 1001 GENOMES BROWSER]. Great source of data for natural variation analysis.


Genome-wide distribution of many diagnostic chromatin marks in Arabidopsis can be seen at the websites run by the Jacobsen/Pellegrini's labs [http://epigenomics.mcdb.ucla.edu/DNAmeth/ 'UCLA Epigenome'] or SALK institute  [http://neomorph.salk.edu/epigenome/epigenome.html 'SALK Epigenome'].
[http://epigenomics.mcdb.ucla.edu/DNAmeth/ 'UCLA Epigenome'], [http://neomorph.salk.edu/epigenome/epigenome.html 'SALK Epigenome']. Genome-wide distribution of many diagnostic chromatin marks in Arabidopsis at the websites run by the Jacobsen/Pellegrini's labs  or SALK institute, respectively.


==R==
==R==
[http://www.r-project.org/ R] and [http://rstudio.org/ RSTUDIO]. Downloads, documentation, help etc.
[http://www.r-project.org/ R] and [http://rstudio.org/ RSTUDIO]. Downloads, documentation, help etc.
Some easy to understand help can be found also on [http://www.statmethods.net/index.html Quick-R].
Some easy to understand help can be found also on [http://www.statmethods.net/index.html Quick-R].

Revision as of 12:29, 7 June 2012


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Publicly Available Arabidopsis Software Tools

TAIR. The basic source of information (not only) for Arabidopsis.

AtENSEMBL. Basic Arabidopsis genome browser. Handy for checking available mutants and their quick ordering because of link to the NASC collections.

SALK SIGnAL. Bunch of resources for Arabidopsis work, e.g. T-DNA orientation finder, 'SALK Epigenome' etc.

1001 GENOMES, SALK 1001 GENOMES BROWSER. Great source of data for natural variation analysis.

'UCLA Epigenome', 'SALK Epigenome'. Genome-wide distribution of many diagnostic chromatin marks in Arabidopsis at the websites run by the Jacobsen/Pellegrini's labs or SALK institute, respectively.

R

R and RSTUDIO. Downloads, documentation, help etc. Some easy to understand help can be found also on Quick-R.

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