- fix: fixed x-axis direction annotation for volcano plot on contrast
- fix: solved bug in DA when missing contrast level in modelled feature (issue #65).
- Add link to Leduc SCP.replication vignette.
- test: added unit tests for scplainer: ScpModel-Class, scpModelFit-Class, ScpModel-Workflow
- New Bioconductor 3.20 (devel) release
- New Bioconductor 3.19 (stable) release
- fix: fixed small error in degrees of freedom
- fix: break workflow upon infinite values
- fix: first drop variable before centering numerical variables (see #54)
- Refactor
readSCP()
andreadSCPFromDIANN()
to use new QFeatures implementations.
- New scplainer workflow and citation
- Add
addReducedDims()
(see #52) - fix: logFC and associated SE are now correctly computed
- docs: fixed vignette about reporting missing values
- docs: add a QFeatures figure to the nutshell vignette
- New Bioconductor 3.18 (devel) release
- New Bioconductor 3.18 (stable) release
- Major feat: added SCP data modelling workflow + documentation
- feat: added readSCPfromDIANN() that creates a QFeatures object from DIANN output tables.
- Nothing yet.
- 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.
- Updated citation
- New Bioconductor 3.18 (devel) release
- New Bioconductor 3.17 (stable) release
- Updated citation
- Fix minor typo in
readSCP()
man page
- New Bioconductor 3.17 (devel) release
- New Bioconductor 3.16 (stable) release
- Updated CITATION
- Added sticker
- Updated CITATION
- refactor: package complies with BiocCheck
- docs: fixed bug in vignette
- Add CC-BY-SA license for vignettes.
- 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.
- New devel (Bioc 3.16)
- New stable release (Bioc 3.15)
- Added CITATION <2021-10-29>
- New devel (Bioc 3.15)
- New stable release (Bioc 3.14)
- docs: included
QFeatures
plot in the vignette - docs: created a vignette about advanced usage of
scp
- 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
- refactor: deprecated
rowDataToDF
. This function is now replaced byQFeatures::rbindRowData
.
- New devel (Bioc 3.14)
- New stable release (Bioc 3.13)
- feature:
readSCP
now allows for asuffix
argument to better customize the sample names. <2021-03-17>
- 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
. TheSCoPE2
normalization method can now reproduce the results from SCoPE2. <2021-02-19> - docs: improved vignette <2021-02-16>
- feat: added a
rowDataName
argument tocomputeSCR
<2021-02-08>
- 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 inreadSCP
to automatically remove columns that contain only NA's <2021-02-06>
- 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 topep2qvalue
. This is more in line with the theory. Also adapted the unit tests. <2021-01-23>
- docs: improved the description of the
scp
data structure in the vignette <2021-01-05> - refactor: renamed the
groupCol
togroupBy
andpepCol
toPEP
incomputeFDR
. <2020-12-08> - refactor: renamed
computeMedianCV
tocomputeMedianCV_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 calledmedianCVperCell
. See issue#7 for more information <2020-12-07>
- Fix news file
- New devel (Bioc 3.13)
- New stable release (Bioc 3.12)
- Update installation instructions <2020-10-14 Wed>
- 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 theDESCRIPTION
file and adapted the data loading (egdata(scp1)
todata("scp1")
) <2020-10-13 Tue> - Documentation: added data collection description for the 3 example datasets <2020-10-13 Tue>
- fix:
computeFDR
can handle missing values (see issue #12) <2020-10-02 Fri>
- Maintainer subscribed to bioc-devel mailing list
- Removed
infIsNA
, the implementation was moved to theQFeatures
packages
- Bioconductor submission