Pecinka Lab:Resources: Difference between revisions
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[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. | [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. | ||
[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. | [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 the 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 06:00, 8 June 2012
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Centre of Plant Structural and Functional Genomics |
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.
EXPRESSION DATA in eFP BROWSER. Even your grandma will understand gene expression with this tool.
GENEVESTIGATOR. Gene expression analysis center containing more datasets than eFP browser and also several other tools. Requires registration.
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 the SALK institute, respectively.
R
R and RSTUDIO. Downloads, documentation, help etc. Some easy to understand help can be found also on Quick-R.
