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Adobe PDF - 170.9 KB - MD5: 8f2156ddb6bc3002afde1dcb81d9828c
This markdown contains code to generate within clad comparisons (monogamous vs. non-monogamous) of expression and divergence time (euclidean distance), expression and mating charactaristics (euclidean distance), and phylogenetic independent contrast of expression PC1 and mating
Adobe PDF - 156.0 KB - MD5: 7cec61740bc2c7adda003b2749706af1
These scripts assess differential expression between monogamous and non-monogamous species between all clades and across evolutionary subgroupings. Different approaches to differential expression analysis were used to identify novel candidates associated with monogamy. --RRHO.htm...
Adobe PDF - 154.5 KB - MD5: 85046e5674d8f0dc78d700af2ff4b5b8
Integrate Log2 fold difference, DESeq2 all vertebrates, and RRHO most up- and down-regulated genes to generte a heatmap of novel candidates
Adobe PDF - 150.2 KB - MD5: afbf4a09d852922c861a5769763e165e
R script that finds the gene with the largest log2fold change for each clade (positive or negative)using the normalized RPM, filters the name of that gene and generates a data frame with OrthoGroup, MaxLFC, and raw counts for these representative genes/OGGs for each species. In a...
Adobe PDF - 138.0 KB - MD5: 20a479153b7705983967fe0f4d917d07
R script that (1) generate a data frame for each species with raw reads and read per million (RPMs) for genes assigned to an OGG, and (2) identify the number of genes that overlap within a clade and the number of OGGs that overlap between clades.
MS Excel - 79.0 KB - MD5: ff83a82db79e36894349146dfc0c0735
MS Excel - 160.0 KB - MD5: f7e2417241064c1356d15f815374c173
MS Excel - 229.5 KB - MD5: f8b0cdadf692eb7e75eff5def5205f5d
MS Excel - 173.0 KB - MD5: 0835bf0ccf9dce742b3229f5a6cc6b42
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