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Move to a single report template #19

Merged
merged 100 commits into from
Apr 29, 2024
Merged

Move to a single report template #19

merged 100 commits into from
Apr 29, 2024

Commits on Oct 13, 2023

  1. Version bump

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  2. First iteration of DIA-NN output support

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    csoneson committed Oct 13, 2023
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  3. Include more file types for DIA-NN import

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    csoneson committed Oct 13, 2023
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  4. Add DIA-NN reference

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    csoneson committed Oct 13, 2023
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  5. Add DIA-NN pr_matrix and main report for testing purposes

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    csoneson committed Oct 13, 2023
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  6. Add Tobias as contributor

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Commits on Oct 15, 2023

  1. Document DIA-NN-related functions, expand list of supported file types

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Commits on Oct 20, 2023

  1. Add function to read DIA-NN log

    @csoneson
    csoneson committed Oct 20, 2023
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  2. Add DIA-NN info to report

    @csoneson
    csoneson committed Oct 20, 2023
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  3. Fix paths, separate cmd from other settings

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    csoneson committed Oct 20, 2023
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Commits on Oct 27, 2023

  1. Add tests for DIA-NN functionality

    @csoneson
    csoneson committed Oct 27, 2023
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  2. Fix documentation

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    csoneson committed Oct 27, 2023
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Commits on Oct 30, 2023

  1. Bump version

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    csoneson committed Oct 30, 2023
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  2. Create first version of unified template (copy MQ template)

    @csoneson
    csoneson committed Oct 30, 2023
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  3. Generalize initial sentence

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    csoneson committed Oct 30, 2023
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  4. Consolidate run info table chunk

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    csoneson committed Oct 30, 2023
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  5. Make iColPattern inclusion dependent on expType

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    csoneson committed Oct 30, 2023
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  6. Consolidate text about input file

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    csoneson committed Oct 30, 2023
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  7. Consolidate data import chunk

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    csoneson committed Oct 30, 2023
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  8. Simplify text about sample names

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    csoneson committed Oct 30, 2023
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  9. Consolidate filtering chunk

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    csoneson committed Oct 30, 2023
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  10. Intermediate metadata list

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    csoneson committed Oct 30, 2023
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  11. Additional adaptations to consolidate FragPipe template

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    csoneson committed Oct 30, 2023
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  12. Additional adaptations to consolidate PD template

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    csoneson committed Oct 30, 2023
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  13. Update NEWS

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    csoneson committed Oct 30, 2023
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  14. Update default templateRmd

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    csoneson committed Oct 30, 2023
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  15. Add expType argument

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    csoneson committed Oct 30, 2023
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  16. Add tests

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    csoneson committed Oct 30, 2023
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  17. Remove specific templates

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    csoneson committed Oct 30, 2023
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Commits on Nov 1, 2023

  1. Fix variable name

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    csoneson committed Nov 1, 2023
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Commits on Jan 27, 2024

  1. Fix DIANN example

    @csoneson
    csoneson committed Jan 27, 2024
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  2. Adapt missing value plots to work with both percentages and proportions

    @csoneson
    csoneson committed Jan 27, 2024
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  3. Fix tidyselect warnings

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    csoneson committed Jan 27, 2024
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  4. Replace ggseqlogo (removed from CRAN) with motifStack

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    csoneson committed Jan 27, 2024
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  5. Swap ggseqlogo (removed from CRAN) for motifStack; adapt missing valu… 

    …e plots to work with both percentages and proportions.

Merge branch 'diann' into single-rep

# Conflicts:
#	DESCRIPTION
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  6. Edit NEWS

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Commits on Jan 29, 2024

  1. Fix sample name column for DIANN import

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    csoneson committed Jan 29, 2024
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  2. Fix sample column name in DIA-NN import

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    csoneson committed Jan 29, 2024
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Commits on Feb 2, 2024

  1. Fix DIANN log file reading to handle vectors of modifications.

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    csoneson committed Feb 2, 2024
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  2. Adapt DIA-NN log import to handle vector output 

    Merge branch 'diann' into single-rep

# Conflicts:
#	DESCRIPTION
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Commits on Feb 13, 2024

  1. Fix reference to 'Show' buttons

    @csoneson
    csoneson committed Feb 13, 2024
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  2. Remove samples with no detected features

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    csoneson committed Feb 13, 2024
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  3. Rerender documentation

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    csoneson committed Feb 13, 2024
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  4. Make sure that the feature displayed by default in the heatmap has at… 

    … least one observed value
    @csoneson
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  5. Add argument addHeatmap to run functions

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    csoneson committed Feb 13, 2024
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  6. Update NEWS

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    csoneson committed Feb 13, 2024
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  7. Make run*Analysis() functions inherit applicable parameters from runM… 

    …axQuantAnalysis()
    @csoneson
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  8. Document missing arguments for text snippets

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    csoneson committed Feb 13, 2024
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  9. Add text snippets for Spectronaut

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    csoneson committed Feb 13, 2024
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  10. Add Spectronaut support in prepareFinalSCE

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    csoneson committed Feb 13, 2024
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  11. Adapt template report to allow Spectronaut output

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    csoneson committed Feb 13, 2024
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  12. Add importSpectronaut function

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    csoneson committed Feb 13, 2024
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  13. Add checkArgumentsSpectronaut function

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  14. Add runSpectronautAnalysis function

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    csoneson committed Feb 13, 2024
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  15. Update NEWS

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    csoneson committed Feb 13, 2024
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Commits on Feb 16, 2024

  1. Use correct assay

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    csoneson committed Feb 16, 2024
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Commits on Feb 20, 2024

  1. Manually add selected Spectronaut annotation columns

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Commits on Feb 21, 2024

  1. Add function to filter decoys in Spectronaut data

    @csoneson
    csoneson committed Feb 21, 2024
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  2. Fix handling of missing values in Spectronaut import

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    csoneson committed Feb 21, 2024
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Commits on Mar 3, 2024

  1. Add extraFeatureCols argument

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    csoneson committed Mar 3, 2024
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Commits on Mar 5, 2024

  1. Add support for displayName column in sample annotation table

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    csoneson committed Mar 5, 2024
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  2. Fix printing of feature names

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    csoneson committed Mar 5, 2024
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Commits on Mar 12, 2024

  1. Read information about Top N ions for FragPipe

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    csoneson committed Mar 12, 2024
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  2. Fix unit tests

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    csoneson committed Mar 12, 2024
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Commits on Mar 28, 2024

  1. Version bump

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    csoneson committed Mar 28, 2024
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  2. Add extracts from hu.MAP 2.0 and the Complex Portal

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    csoneson committed Mar 28, 2024
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  3. Update script for generating complex db

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    csoneson committed Mar 28, 2024
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  4. Expand set of complexes included in database

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  5. Add expanded complex db

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    csoneson committed Mar 28, 2024
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  6. Update NEWS

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  7. Hide box plot legends if there are too many groups

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    csoneson committed Mar 28, 2024
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  8. Update default complex db

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    csoneson committed Mar 28, 2024
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Commits on Apr 1, 2024

  1. Add MinProbGlobal imputation method

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  2. Add some more tests

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    csoneson committed Apr 1, 2024
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  3. Fix argument check

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    csoneson committed Apr 1, 2024
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Commits on Apr 6, 2024

  1. Make readFragPipeInfo() more robust against possible repeated lines i… 

    …n the config file
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Commits on Apr 8, 2024

  1. Add makeInteractiveVolcano argument to plotVolcano()

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Commits on Apr 22, 2024

  1. Version bump

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    csoneson committed Apr 22, 2024
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  2. Add details about DIA-NN command line to report

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    csoneson committed Apr 22, 2024
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Commits on Apr 23, 2024

  1. Fix typo

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    csoneson committed Apr 23, 2024
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  2. Propagate ... also to impSeqRob

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  3. Add column with links to ComplexPortal query to link table

    @csoneson
    csoneson committed Apr 23, 2024
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  4. Add note about DIA-NN and Spectronaut support

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    csoneson committed Apr 23, 2024
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  5. Move collapsing earlier in readFragPipeInfo

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    csoneson committed Apr 23, 2024
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  6. Include pathways from MSigDB among supported feature collections

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Commits on Apr 26, 2024

  1. Fix Spectronaut processing of columns with all NAs

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Commits on Apr 28, 2024

  1. Make sure DIA-NN example data files uses the same scientific notation… 

    … as those output directly from DIA-NN
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  2. Expand documentation of DIA-NN example data, explaining the subsettin… 

    …g that was done.
    @csoneson
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  3. Update NEWS

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  4. Normalize input data paths

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  5. Add example for DIA-NN on main report

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  6. Allow proteinIdCol to be NULL

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    csoneson committed Apr 28, 2024
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  7. Move path normalization

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  8. Add support for Spectronaut PG columns in importExperiment

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    csoneson committed Apr 28, 2024
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  9. Add support for Spectronaut PG pivot files

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  10. Fix typo

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  11. Reorder Spectronaut assays to have the one corresponding to aName first

    @csoneson
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  12. Add initial support for reading Spectronaut log files

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Commits on Apr 29, 2024

  1. Manually clear cache on GHA, use newer Docker container

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  2. Increase tolerance in normalization test (for M1)

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