Differential expression runs with DESeq2. Link to code.
[Read More]
00 - Size Distribution - CEABiGR lncRNA
Size distribution figures of CEAGBiGR lncRNAs. Link to code.
[Read More]
00 - Status - e5 3 Species lncRNA Comparative
Current status of e5 3 species lncRNA comparative work from SICB slides
[Read More]
CEABiGR lncRNA - WGCNA-01
Running Ariana’s version which has much more stringent filtering steps before performing the WGCNA:
Removing genes that don’t show any expression (done in previous WGCNA)
Choosing how many 0s to allow per gene
Choosing expression level thresholds
[Read More]
CEABiGR lncRNA - WGCNA-00
Running individual WGCNA analyses on male and female sets of oysters. Initial code can be found here.
General notes about first run:
Using signed networks (those that take into account the direction of expression as well as the value of the count - up or down)
Blockwise clustering for module formation, usually good for large datasets, probably not necessary since there isn’t too much data
Current status: Switched from this analysis at module merging stage since none of the modules merged with a stringent similarity setting
[Read More]