Using Named Pipes and Process Substitution

Little known UNIX features to avoid writing temporary files in your data pipelines explained by Vince Buffalo in his digital notebook. Introducing named pipes and process substitution.
Location: Saint Kilda VIC 3182, Australia

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Data analysis step 8: Pathway analysis with GSEA

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In our RNA-seq series so far we've performed differential analysis and generated some pretty graphs, showing thousands of differentially expressed genes after azacitidine treatment. In order to understand the biology underlying the differential gene expression profile, we need to perform pathway analysis. We use Gene Set Enrichment Analysis ( GSEA ) because it can detect pathway changes more sensitively and robustly than some methods. A 2013 paper compared a bunch of gene set analyses software with microarrays and is worth a look. Generate a rank file The rank file is a list of detected genes and a rank metric score. At the top of the list are genes with the "strongest" up-regulation, at the bottom of the list are the genes with the "strongest" down-regulation and the genes not changing are in the middle. The metric score I like to use is the sign of the fold change multiplied by the inverse of the p-value, although there may be better methods out there...
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Uploading data to GEO - which method is faster?

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Generating a custom gmt file for gene set analysis

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Pathway and gene set analysis is a common procedure for interpretation of RNA-seq or other genome-wide expression assays. Most of the time, we use GSEA to tell us whether our gene sets of interest are up- or down-regulated. We can use gene sets from KEGG , Reactome , GO ,  MSigDB  and other sources, but you can also generate your own gene sets. The format used for GSEA is gmt . I'm going to take you through two examples of generating custom gene sets: Generate gene sets from published data sets using GEO2R Let's say you're interested in the transcription factor STAT1. I found a dataset in GEO called "Knockdown of STAT1 in SCC61 tumor xenografts leads to alterations in the expression of energy metabolic pathways", which has a paper in BMC Med.  Most uploaded array data sets can be reanalysed with GEO2R, which runs the array analysis tool Limma but this is embedded in the webpage and has a GUI which makes it very accessible for biologists. Click this link ...
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