NEWS
Damsel 0.8
- removed deprecated functions
- removed old function names
Damsel 0.7.1
- new Bioconductor style names for functions alongside original function names
- updated gene ontology plot
Damsel 0.7.0
New features
- updated gene ontology output of results
- gene ontology plot fn
plot_gene_ontology()
- all functions operate case-insensitive - allow for .bam or .BAM and same with
dam or Dam
- replaced "Downreg" meth_status with "No_sig"
- new peak function available
- updates to plot functions - fixed wrap plot, set colours for count plot
- added new gene fn that uses a TxDb object or biomaRt (get_genes_biomaRt has been deprecated and will be removed)
- example count data available through data(dros_counts)
Damsel 0.6.0
Removed features
- removed process_bams_old as dependency
exomeCopy has been deprecated.
Damsel 0.5.0
Removed features
- regions_gatc_drosophila_dm6 is no longer available as a data file upon loading.
Can be made with
gatc_region_fn()
Damsel 0.4.0
New features
- process_bams() new count method using
Rsubread::featureCounts() allowing for fractional counts and differentiating between single and paired end BAM files
- edgeR_set_up() filter out large regions (> 10kb)
- aggregate_peaks() new method for ranking peaks based on theory of
csaw::getBestTest()
- aggregate_peaks() retain small peaks so that they are able to be combined with the gaps fn
- gatc_track() simplified for one argument input - identifies if input is BSgenome or FASTA
Bug fixes
- geom_genes can now handle a region of only introns - previously threw an error
Damsel 0.3.1
New features
- Plotting options - counts layout and log2 scale, and peak_id text
- New default for differential testing: p-value set to 0.01
Damsel 0.3.0
Bug fixes
- streamlined outputs
- removed obselete functions
Damsel 0.2.0
New features
- New peak output and functionality (combines peaks with small gaps)
- New genes output - with list of 3 data.frames
- Gene ontology fn
- Plot_wrap() - plot all at once
- gatc_track() - create the GATC track
Bug fixes
Documentation
Damsel 0.1.0
- Added a
NEWS.md file to track changes to the package.
- Added geom_genes.me allowing for genes plot
- Fixed geom_peak.new