Changes in version 1.13
scp 1.13.6
(nothing yet)
scp 1.13.5
- fix: fixed small error in degrees of freedom
- fix: break workflow upon infinite values
scp 1.13.4
- fix: first drop variable before centering numerical variables (see
#54)
scp 1.13.3
- Refactor readSCP() and readSCPFromDIANN() to use new QFeatures
implementations.
scp 1.13.2
- New scplainer workflow and citation
- Add addReducedDims() (see #52)
- fix: logFC and associated SE are now correctly computed
scp 1.13.1
- docs: fixed vignette about reporting missing values
- docs: add a QFeatures figure to the nutshell vignette
scp 1.13.0
- New Bioconductor 3.18 (devel) release
Changes in version 1.12
scp 1.12.0
- New Bioconductor 3.18 (stable) release
scp 1.11.3
- Major feat: added SCP data modelling workflow + documentation
- 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