Major work flow
Core analysis Tox analysis Metabolomic analysis Biomarker filter Filter dataset microRNA target filter
Major work flow
Core analysis Tox analysis Metabolomic analysis Biomarker filter Filter dataset microRNA target filter
When I was working on Mehmet’s miRNA data (from Affymetrix miRNA-3.0 array), I encountered an error. It turns out that I need to install new library to read in .cdf platform.
source("http://bioconductor.org/biocLite.R") biocLite("pd.mirna.3.0")
With miRBase mysql local set up, I can easily search for miRs. i.e.
select * from mirna_mature where mature_name like "mmu-miR-15b%" ; +-------------+----------------+--------------------+--------------+--------------+-----------------------------------------------------------------------------------+------------+ | auto_mature | mature_name | previous_mature_id | mature_acc | evidence | experiment | similarity | +-------------+----------------+--------------------+--------------+--------------+-----------------------------------------------------------------------------------+------------+ | 75243 | mmu-miR-15b-3p | mmu-miR-15b* | MIMAT0004521 | experimental | cloned [17604727], Solexa [20215419,20413612] | | | 75242 | mmu-miR-15b-5p | mmu-miR-15b | MIMAT0000124 | experimental | cloned [12007417,12919684,15538371,16766679,17604727], Solexa [20215419,20413612] | | +-------------+----------------+--------------------+--------------+--------------+-----------------------------------------------------------------------------------+------------+