v3.2.5

What's Changed

• release v3.2.5 by @leahkemp in #13

Full Changelog: 3.2.4...3.2.5

Notable changes

rna_species_composition:

• differentiate titles between docs
• put samples first in column since it's the main variable of interest
• add percentages of RNA's identified into tables
• update description

sequencing_read_qc:

• plot only raw sequencing read count and RNA counts by pipeline

v3.2.4

What's Changed

• release v3.2.4 by @leahkemp in #12

Full Changelog: 3.2.3...3.2.4

Notable changes

• fix reading metadata file
• fix matching of samples to mapping rates data

v3.2.3

What's Changed

• release v3.2.3 by @leahkemp in #11

Full Changelog: 3.2.2...3.2.3

Notable changes

• further split differential expression documents for faster HTML loading
• improve matching of samples to mapping rates data

v3.2.2

What's Changed

• release v3.2.2 by @leahkemp in #10

Full Changelog: 3.2.1...3.2.2

Notable changes

• fix xaxis label in expression plotting app
• separate diff expr docs for faster html loading

v3.2.1

What's Changed

• release v3.2.1 by @leahkemp in #9

Full Changelog: 3.2.0...3.2.1

Notable changes

• patch fix

v3.2.0

What's Changed

• release v3.2.0 by @leahkemp in #8

Full Changelog: 3.1.1...3.2.0

Notable changes

• allow up to 10 treatment comparisons/contrasts
• add sanity check for the number of contrasts user specifies in the configuration file

v3.1.1

What's Changed

• release 3.1.1 by @leahkemp in #7

Full Changelog: 3.1.0...3.1.1

Notable changes

• not all HTML files for the example webpage were updated

v3.1.0

What's Changed

• release v3.1.0 by @leahkemp in #6

Full Changelog: 3.0.0...3.1.0

Notable changes

• 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

v3.0.0

What's Changed

• release v3.0.0 by @leahkemp in #5

Full Changelog: 2.1.2...3.0.0

Notable changes

• fix conditional r chunk eval vector
• add output dirs for result files
• allow the use of additional variables in metadata (namely in the RNA expression plotting app)
• use RDS objects to reduce duplicate computation
• fix table labels (RNA expression plotting app)
• add automatic scaling for plots with diff num samples
• remove need to specify the order of the treatment groups in expression plotting app in config file (breaking change)
• improve tooltips

v2.1.2

What's Changed

• release v2.1.2 by @leahkemp in #4

Full Changelog: 2.1.1...2.1.2

Notable changes

• improve figure control of heatmaps
• make heatmap plot widths scale to treatment groups of different sizes
• fix links to RNA species composition docs
• fix conditional r chunk evaluation list