Update Seqinfo-holding serialized object(s) to reflect new location of Seqinfo class definition (the class was recently moved from GenomeinfoDb to the new Seqinfo package). Hervé Pagès
scp 1.19.4
Update scplainer reference.
scp 1.19.3
docs: explicitly mention scplainer in the man pages
scp 1.19.2
feat: improved error message when pattern is not found in computeSCR
Recommend the use of SummarizedExperiment instead of SingleCellExperiment for performance reasons.
All functions are now compatible with SummarizedExperiment.
data("scp1") now contains SummarizedExperiment objects.
By default, readSCP and readSCPfromDIANN now create QFeatures objects that contain SummarizedExperiment objects.
readSCP and readSCPfromDIANN have a new parameter: experimentsAsSce that indicate if the QFeatures should contain SingleCellExperiment, default is FALSE.
readSCP and readSCPfromDIANN now return a QFeatures of type “scp”.
scpModelWorkflow now automatically convert a SummarizedExperiment to a SingleCellExperiment.
scp 1.16
scp 1.16.0
New Bioconductor 3.20 release
scp 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
scp 1.14
scp 1.14.0
New Bioconductor 3.19 (stable) release
scp 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.
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
scp 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
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>