RNA-seq
Draws the last RNA-seq run: the volcano, MA plot or dispersion fit of a differential-expression run, the strongest over-represented gene sets, or one gene set's running enrichment score along the ranking.
What it does
Opens beside the RNA-seq panel when a question runs, and redraws when another runs. Every mark is a value the run returned; hover a gene for its fold change and adjusted p, and choose a gene or a set to pick out the same row in the panel's table.
What this computes
- the volcano: every tested gene at its log2 fold change and −log10 p-value, up-regulated significant genes in one colour, down-regulated in another, the rest muted
- the MA plot: log2 fold change against the log10 mean of normalized counts, with the line of no change
- the dispersion fit: each gene's gene-wise dispersion estimate, the fitted trend and the final shrunken dispersion against mean count, on log scales
- the strongest gene sets: the sets with the smallest adjusted p, as −log10 adjusted p with each set's gene ratio, the over-represented ones marked and the cutoff drawn
- the running enrichment score: the score of the set you choose at every rank of the ordered list, its peak marked, a tick for every member gene beneath it, and the ranking statistic itself below, so the leading edge reads as the members before the peak
Population genetics
Draws the last population-genetics run: sites along the chromosome, the pairwise LD matrix, samples in principal-component space with the scree, or one ancestry bar per sample with the cross-entropy by K.
Site avoidance heat map
Draws the last site-avoidance sweep: every record against every recognition site, coloured by how far its count sits below or above the null.