seqCAT version 1.6.0

This is the fourth release of the seqCAT package, which follows Bioconductor's "even-release, odd-devel" version scheme and is equivalent to the 1.6.0 release on the Bioconductor website. It includes the following additions and changes:

• Rename several function arguments to increase clarity
• Make filtering of variant calling-specific quality metrics optional
• Add a check to validate if input VCFs are genomic VCFs
• Add checks to validate if input VCFs contain data on variant depth, allelic depth and genotype data

seqCAT version 1.4.1

This version (also available in devel-1.5.2) makes seqCAT compatible with the 0.8.0 version of the dplyr package, which introduced changes that broke earlier versions.

seqCAT version 1.4.0

This is the third release of the seqCAT package, which follows Bioconductor's "even-release, odd-devel" version scheme and is equivalent to the 1.4.0 release on the Bioconductor website. It includes the following additions and changes:

• Added convenience functions for creating and reading multiple SNV profiles
• Added functionality for reading general COSMIC mutational data, not just cell line mutational data
• Fixed an issue when reading COSMIC data due to new GRanges functionality
• Updated the citation info with the now-published seqCAT-specific article

seqCAT version 1.2.1

This version (also available in devel-1.3.3) makes seqCAT compatible with the 2.3.0 version of the ggplot package, which introduced changes that broke earlier versions.

seqCAT version 1.2.0

This is the second release of the seqCAT package, which follows Bioconductor's "even-release, odd-devel" version scheme and is equivalent to the 1.2.0 release on the Bioconductor website. It includes the following additions and changes:

• Add functionality for analysing VCF files containing unannotated variants
• Add functionality for listing non-overlapping variants between profiles
• Mitochondrial variants can now be optionally skipped when reading SNV
  profiles in the read_variants function
• Add the list_variants function for listing the genotypes of
  user-specified variants in each provided SNV profile
• Add the plot_variant_list function for plotting a genotype grid for
  each variant output by the list_variants function
• Fix a multi-sample VCF profile creation issue (python only)
• Reading zero-variant profiles now properly returns a GRanges object with
  a dummy-variant profile containing the sample name
• Enable the plot_impacts function to properly analyse multi-impact SNVs
• Fix reading of SNV profiles containing single-quoted strings

seqCAT version 1.0.0

This is the very first release of the seqCAT R package, and mirrors the 1.0.0 version available on Bioconductor. The original functionality include the following:

• Creation of SNV profiles from annotated VCF files
• Reading and exploring SNV profiles
• Comparing and evaluating SNV profiles
• Exploring both known variants and specific genomic regions of interest
• Creation of both similarity heatmaps and impact distribution figures
• Convenience functions for performing both one-to-many and many-to-many profile comparisons