NEWS

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scp 1.21

scp 1.21.1

• Update Chris' email address.

scp 1.21.0

• New Bioconductor devel

scp 1.19

scp 1.19.5

• 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
• feat: use typeMetadata (based on QFeatues 1.19.1)

scp 1.19.1

• fix: moved from the deprecated longFormat() to longForm()
• doc: fixed readSingleCellExperiment example (see #94)
• doc: minor documentation recompilation

scp 1.19.0

• New Bioconductor 3.22 release

scp 1.18

scp 1.18.0

• New Bioconductor 3.21 release

scp 1.17

scp 1.17.0

• New Bioconductor 3.21 devel

scp 1.17.1

• Deprecate aggregateFeaturesOverAssays, use QFeatures::aggregateFeatures instead.

scp 1.17.2

• 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.

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

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
• fix failing unit test.

scp 1.11.1

• Updated citation

scp 1.11.0

• New Bioconductor 3.18 (devel) release

scp 1.10

scp 1.10.0

• New Bioconductor 3.17 (stable) release

scp 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

scp 1.8

scp 1.8.0

• New Bioconductor 3.16 (stable) release

scp 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)

scp 1.6

• New stable release (Bioc 3.15)

scp 1.5

scp 1.5.1

• Added CITATION <2021-10-29>

scp 1.5.0

• New devel (Bioc 3.15)

scp 1.4

• New stable release (Bioc 3.14)

scp 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)

scp 1.2

• New stable release (Bioc 3.13)

scp 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)

scp 1.0

scp 1.0.0

• New stable release (Bioc 3.12)

scp 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