Changes in version 1.15 scp 1.15.2 - 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. scp 1.15.1 - test: added unit tests for scplainer: ScpModel-Class, scpModelFit-Class, ScpModel-Workflow scp 1.15.0 - New Bioconductor 3.20 (devel) release Changes in version 1.14 scp 1.14.0 - New Bioconductor 3.19 (stable) release Changes in version 1.13 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