NEWS.md

In AngelCampos/tx_tools: An R package facilitating analysis of RNA modifications, structures, and interactions

txtools 1.0.5

• Added the loadSecondaryAligns argument to tx_load_bam() so that secondary alignments can be easily discarded by setting it to FALSE. The same effect can be accomplished by inputing a scanFlag built with the Rsamtools::scanBamFlag() helper, but this way it is a more streamlined feature.

txtools 1.0.4

• Added tx_combineTxReads() to combine reads processed by tx_reads().
• Setup pkgdown website.
• Bug fix: Loading Bed-6 gene annotations broke due to a dependency update.

txtools 0.1.2

• Bug fix: stringr::str_sub() update broke functions.

txtools 0.1.1

• Bug fix: Error processing single-end reads

txtools 0.1.0

• Major:
  • 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.

txtools 0.0.8

• 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().

txtools 0.0.7

• 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.

txtools 0.0.6

• 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.

txtools 0.0.5

• 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.

txtools 0.0.4

• Uni and Multi-core functions merged into unique functions capable of using multi-cores with the parallel package.

txtools 0.0.3

• Bug fixed when using BED6 annotation

txtools 0.0.2

• Updating plotting function tx_plot_staEndCov() to remove coverage counts.
• Other minor changes

txtools 0.0.1

• Initial draft of package

AngelCampos/tx_tools documentation built on Sept. 17, 2024, 1:27 a.m.