scp 1.3

scp 1.3.3

  • docs: included QFeatures plot in the vignette
  • docs: created a vignette about advanced usage of scp

scp 1.3.2

  • feat: computeSCR now allows for user supplied function that will summarize the values from multiple samples and multiple carrier.
  • docs: used more standard variable names in scp vignette.
  • docs: created a QFeatures recap vignette

scp 1.3.1

scp 1.3.0

  • New devel (Bioc 3.14)

scp 1.2

  • New stable release (Bioc 3.13)

scp 1.1

scp 1.1.6

  • feature: readSCP now allows for a suffix argument to better customize the sample names. <2021-03-17>

scp 1.1.5

  • deprecation: thanks to the new normalization method in medianCVperCell, ‘computeMedianCV_SCoPE2’ is now deprecated and should no longer be used. <2021-02-19>
  • feat: added a new normalization method to medianCVperCell. The SCoPE2 normalization method can now reproduce the results from SCoPE2. <2021-02-19>
  • docs: improved vignette <2021-02-16>
  • feat: added a rowDataName argument to computeSCR <2021-02-08>

scp 1.1.4

  • fix: removed bug in vignette header <2021-02-06>
  • data: update the example data with the latest release of SCoPE2 <2021-02-06>
  • feat: added removeEmptyCol argument in readSCP to automatically remove columns that contain only NA’s <2021-02-06>

scp 1.1.3

  • docs: improved the manual page for pep2qvalue and the corresponding section in the vignette. <2021-01-23>
  • refactor: reimplemented the computeFDR to catch up with the new release of SCoPE2. computeFDR was renamed to pep2qvalue. This is more in line with the theory. Also adapted the unit tests. <2021-01-23>

scp 1.1.2

  • docs: improved the description of the scp data structure in the vignette <2021-01-05>
  • refactor: renamed the groupCol to groupBy and pepCol to PEP in computeFDR. <2020-12-08>
  • refactor: renamed computeMedianCV to computeMedianCV_SCoPE2 and deprecated the function. The function will be preserved for backward compatibility with the replication of the SCoPE2 analysis (Specht et al. 2020). Instead, a new function is implemented and called medianCVperCell. See issue#7 for more information <2020-12-07>

scp 1.1.1

  • Fix news file

scp 1.1.0

  • New devel (Bioc 3.13)

scp 1.0

scp 1.0.0

  • New stable release (Bioc 3.12)

scp 0.99

scp 0.99.4

  • Update installation instructions <2020-10-14 Wed>

scp 0.99.3

  • fix: solved ‘invalid subsetting’ issue <2020-10-14 Wed>
  • Adapted the vignette to remove warnings and fix missing PCA plot. <2020-10-14 Wed>
  • extended the installation guide, providing both a stable and a devel installation. <2020-10-13 Tue>
  • Removed the LazyLoad from the DESCRIPTION file and adapted the data loading (eg data(scp1) to data("scp1")) <2020-10-13 Tue>
  • Documentation: added data collection description for the 3 example datasets <2020-10-13 Tue>

scp 0.99.2

  • fix: computeFDR can handle missing values (see issue #12) <2020-10-02 Fri>

scp 0.99.1

  • Maintainer subscribed to bioc-devel mailing list
  • Removed infIsNA, the implementation was moved to the QFeatures packages

scp 0.99.0

  • Bioconductor submission