Computational biology and genomics
Check which annotation package you need for your microarray data at http://www.bioconductor.org/packages/release/data/annotation/ The results I’m looking at are from a Illumina HumanHT12v3 BeadChip microarray (illuminaHumanv3.db). Make sure you’re running the latest version of R (R version 2.13.0 (2011-04-13)) and Bioconductor (Bioconductor version 2.8). Sourced from Bioconductor mailing list thread -> [BioC] [Fwd: help in annotation…
Updated: 2013 December 16th to include the Reactome database Source: Bioconductor mailing list: thread [BioC] How to quikly know whether two genes are in the same pathway or not? Using reactome If you ran the above code, you should get this warning: KEGG.db contains mappings based on older data because the original resource was removed…
First download the relevant tables from here. Download tss_library_expr_summary.tsv.bz2, tss_summary.tsv.bz2 and rna_lib_summary.tsv.bz2 and bunzip2 the files. According to information derived from rna_lib_summary.tsv there are 13,897 CAGE tags from the prostate gland (rna_lib_id = HBA). Double check this: Genomic coordinates of TSSs can be obtained from tss_summary.tsv. Here’s a script which generates bedgraph files of all…
Updated 2014 December 19th The normal or Gaussian distribution is commonly occurring continuous probability distribution. The skewness, which is a measure of symmetry (or there lackof), of a normal distribution is zero since the distribution is symmetrical, i.e. it looks the same to the left and right of the centre. Kurtosis can be used to…
Find genes that are associated with a known gene ontology term: See also: org.Hs.eg.db Source: bioconductor mailing list thread -> [BioC] Query Gene Ontology