Changes in version 1.11                         

scp 1.11.3

  - feat: added readSCPfromDIANN() that creates a QFeatures object from
    DIANN output tables.

scp 1.11.2

  - Nothing yet.

scp 1.11.2

  - feat: added reportMissingValues(), jaccardIndex(),
    cumulativeSensitivityCurve() and predictSensitivity() to facilitate
    reporting missing values. The vignette is also adapted with the new
    functionality.
  - docs: created vignette about reporting missing values in SCP
  - fix failing unit test.

scp 1.11.1

  - Updated citation

scp 1.11.0

  - New Bioconductor 3.18 (devel) release

                        Changes in version 1.10                         

scp 1.10.0

  - New Bioconductor 3.17 (stable) release

                         Changes in version 1.9                         

scp 1.9.2

  - Updated citation

scp 1.9.1

  - Fix minor typo in readSCP() man page

scp 1.9.0

  - New Bioconductor 3.17 (devel) release

                         Changes in version 1.8                         

scp 1.8.0

  - New Bioconductor 3.16 (stable) release

                         Changes in version 1.7                         

scp 1.7.5

  - Updated CITATION
  - Added sticker

scp 1.7.4

  - Updated CITATION

scp 1.7.3

  - refactor: package complies with BiocCheck
  - docs: fixed bug in vignette

scp 1.7.2

  - Add CC-BY-SA license for vignettes.

scp 1.7.1

  - refactor: removed deprecated function rowDataToDF()
  - tests: fixed some tests failing because of SCE version differences.
  - feat: users can now specify sep when sample names are automatically
    generated.

scp 1.7.0

  - New devel (Bioc 3.16)

                         Changes in version 1.6                         

  - New stable release (Bioc 3.15)

                         Changes in version 1.5                         

scp 1.5.1

  - Added CITATION <2021-10-29>

scp 1.5.0

  - New devel (Bioc 3.15)

                         Changes in version 1.4                         

  - New stable release (Bioc 3.14)

                         Changes in version 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

  - refactor: deprecated rowDataToDF. This function is now replaced by
    QFeatures::rbindRowData.

scp 1.3.0

  - New devel (Bioc 3.14)

                         Changes in version 1.2                         

  - New stable release (Bioc 3.13)

                         Changes in version 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)

                         Changes in version 1.0                         

scp 1.0.0

  - New stable release (Bioc 3.12)

                        Changes in version 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>
  - README.md: 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