leahkemp/smncrna_analysis_template: v3.1.0

• release v3.1.0 by @leahkemp in https://github.com/leahkemp/smncrna_analysis_template/pull/6

Full Changelog: https://github.com/leahkemp/smncrna_analysis_template/compare/3.0.0...3.1.0

• account for '.' in RNA names for CSS highlighting
• rename rnas in prepare_counts.R so naming is consistent throughout docs
• remove any rows/RNA's with no counts found in any sample
• remove unnecessary config variable
• restore heatmap plotting to all significance levels
• write files with significant RNA's in diff expression
• account for the situation where there are too many significant RNA's to plot in heatmap
• add sanity checking scripts
• account for data not being analysed when reading rds objects
• ensure datasets not analysed aren't analysed
• increase heatmap height slightly
• account for situation where no datasets are analysed for a given pipeline
• add datasets analysed in diff expression doc
• table formatting and only present num columns in presence/absence doc
• allow the user to set pipeline dirs in config to 'none' (so user can analyse count data from one or both pipelines)
• account for duplicate miRNAs in mds/pca (now if both smrnaseq and exerpt miRNA counts datasets are analysed, only the smrnaseq miRNA count dataset is analysed to avoid duplicate RNA's
• shorten piRNA names for plotting sakes
• seperate differential expression docs for faster html loading
• add some more info to webpage