Added ignore.strand functionality to load reads regardless if the RNA-seq
library is strand-aware.
New plotting function tx_plot_numeric(): Plots numeric variables along
the transcriptomic space.
tx_metagene_() functions have a normalization argument which yields the
are under the curve to be proportional to 1(transcriptomic window length).
Plus minor fixes.
v0.0.8
Fixed loading paired end BAM files when strand sign is defined by read2
("last").
Bugs fixed
Minor improvements:
Loading genome name as first word separated by spaces
Edited main vignette tutorial "txtools"
Added bam2txDT.R script in inst/ dir
Patch 0.0.8.1:
Added "splicingSite" option to tx_get_metageAtCDS() and
tx_plot_metageneAtCDS().
v0.0.7
General Update
Added vignette "txtools_user_guide"
Changed tx_add_diffNucToRef() for tx_add_misincCount()
Changed tx_add_diffNucToRefRatio() for tx_add_misincRate()
Fix minor bugs
0.0.7.4 patch: Fixed a bug that incorrectly included alignments with N
operations in their CIGAR strings (gaps), that didn't match the gene structure.
Removed plotly conversion in tx_plot_*() functions. As can be easily done by
the user with plotly::ggplotly()
0.0.7.8 patch: Fixed tx_orderDT() so that order is not affected by levels
in the 'gene' factor; accordingly fix tx_unifyTxDTL() so DTs have the same
txcoor order. Changing name of function tx_add_misincorpRateNucSpec()
in favor of tx_add_misincRateNucSpec(), so that it conforms to other function
names, former can be used as alias but has been deprecated.
v0.0.6
Fixed a bug detected when loading BAM files with mappings with empty
sequence field
0.0.6.2 patch: Fixed bug related with spurious paired-end alignments, R1 and
R2 order is wrong.
v0.0.5
Update Bioconductor remotes.
Adding tx_core_mc() which is deprecated as alias of tx_reads().
Fix bug in tx_complete_DT() which added refSeq before necessary.
v0.0.4
Uni and Multi-core functions merged into unique functions
capable of using multi-cores with the parallel package.
v0.0.3
Bug fixed when using BED6 annotation
v0.0.2
Updating plotting function tx_plot_staEndCov() to remove
coverage counts.