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txtools 1.0.6

Removed BiocStyle dependency, by

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