Code

Enable volcano plot with ptm data#530

Code

Merged

JanniRoebbecke merged 107 commits intodevcschlaffner/PROTzilla2:devfrom enable-volcano-plot-with-ptm-datacschlaffner/PROTzilla2:enable-volcano-plot-with-ptm-dataCopy head branch name to clipboardNov 11, 2024

+99-41

Commits

Commits on Mar 23, 2024

• evidence import

  

  janni.roebbecke

  committed
  fa28ee3

• tests

  

  janni.roebbecke

  committed
  2f0c566

Commits on Mar 27, 2024

• filter proteins

  

  janni.roebbecke

  committed
  49be94b

• filter sampels

  

  janni.roebbecke

  committed
  2bdae08

Commits on Mar 31, 2024

• Select Peptides by group or sample for coverage visualisation (#410)

  Show description for 104c49b
  

  antonneubauer

  and

  henninggaertner

  authored
  104c49b

Commits on Apr 3, 2024

• tests for filter_proteins with peptide file

  

  janni.roebbecke

  committed
  9b983dd

• tests for filter_proteins with peptide file, better mock dataframe

  

  janni.roebbecke

  committed
  ba0d58e

• output types

  

  janni.roebbecke

  committed
  f07ff7e

• added testing that only filtered Proteins are removed from peptides_df

  

  janni.roebbecke

  committed
  12c1d5c

• tests for filter_samples with peptide file

  

  janni.roebbecke

  committed
  66cd83b

Commits on Apr 4, 2024

• extract test that peptide filtering matches protein filtering into Method

  

  janni.roebbecke

  committed
  f18c8c4

• Merge branch '456-addapt-outlier-detection-for-peptides' into 454-addapt-filtering-for-peptides

  

  janni.roebbecke

  committed
  16f71ea

• refactor: shortened tests by integrating extracted method and mock data

  

  janni.roebbecke

  committed
  2aedccd

• exclude peptides

  

  janni.roebbecke

  committed
  a297922

Commits on Apr 5, 2024

• tests

  

  janni.roebbecke

  committed
  7d115ff

• minor fixes in test

  

  janni.roebbecke

  committed
  4e738e6

• minor fixes in test

  

  janni.roebbecke

  committed
  d77da64

• fix test that peptide filtering matches protein filtering Method

  

  janni.roebbecke

  committed
  6f7d8f7

• fix test that peptide filtering matches protein filtering Method

  

  janni.roebbecke

  committed
  6f12a76

• fix test that peptide filtering matches protein filtering Method

  

  janni.roebbecke

  committed
  f635008

• fix test that peptide filtering matches protein filtering Method

  

  janni.roebbecke

  committed
  cd8fa06

Commits on Apr 6, 2024

• match mock protein dataframe to mock peptide dataframe

  

  janni.roebbecke

  committed
  f62b4f6

Commits on Apr 7, 2024

• extract test that peptide filtering matches protein filtering into Method

  

  janni.roebbecke

  committed
  1c73f76

• implementation

  

  janni.roebbecke

  committed
  83fd7a5

• tests

  

  janni.roebbecke

  committed
  1766d36

Commits on Apr 9, 2024

• tests improve error logging

  

  janni.roebbecke

  committed
  6584acd

• tests git testing

  

  janni.roebbecke

  committed
  f578555

• peptide import added missing column

  

  janni.roebbecke

  committed
  3bf6a7d

Commits on May 25, 2024

• implements form, form_mapping, method and the actual functionality (untested)

  

  janni.roebbecke

  committed
  92de960

Commits on May 26, 2024

• Merge remote-tracking branch 'refs/remotes/origin/452-import-evidence-file' into peptides

  Show description for 25f15e8
  

  janni.roebbecke

  committed
  25f15e8

Commits on May 27, 2024

• merge peptide filtering

  

  janni.roebbecke

  committed
  2beca7a

Commits on May 28, 2024

• Merge remote-tracking branch 'refs/remotes/origin/456-addapt-outlier-detection-for-peptides' into peptides

  Show description for 0cee245
  

  janni.roebbecke

  committed
  0cee245

• merge peptide filtering and outlier_detection

  

  janni.roebbecke

  committed
  084a10d

• Merge remote-tracking branch 'refs/remotes/origin/455-addapt-transformation-for-peptides' into peptides

  Show description for dc790be
  

  janni.roebbecke

  committed
  dc790be

• merge peptide transformation

  

  janni.roebbecke

  committed
  0e1886a

• implement passing of peptide data between preprocessing steps

  

  janni.roebbecke

  committed
  4733972

• complete implement passing of peptide data between preprocessing steps

  

  janni.roebbecke

  committed
  fd8b555

• implement overhead for new step evidence import

  

  janni.roebbecke

  committed
  e722b27

• Merge branch 'refs/heads/peptides' into filter-peptides-step

  

  janni.roebbecke

  committed
  3a3d68d

• enable selecting multiple proteins of interest and implements tests

  

  janni.roebbecke

  committed
  551916f

Commits on May 29, 2024

• Fix EvidenceImport class (now the right method is called)

  

  janni.roebbecke

  committed
  590396a

• Merge branch 'refs/heads/peptides' into filter-peptides-step

  

  janni.roebbecke

  committed
  04b7e7d

• implement option to choose protein from list of significant proteins

  

  janni.roebbecke

  committed
  b8451a5

• implement option to let the system choose the most expressed protein

  

  janni.roebbecke

  committed
  418eda4

Commits on Jun 4, 2024

• include messages for peptide filtering

  

  janni.roebbecke

  committed
  3da9987

• remove selecting multiple proteins and add substring search

  

  janni.roebbecke

  committed
  0a3ac5c

• add cleaning of protein groups to evidence import

  

  janni.roebbecke

  committed
  1b97ed7

• implement suggested changes: remove default values and correct grammar mistake

  

  janni.roebbecke

  committed
  c90e845

Commits on Jun 5, 2024

• make preprocessing work without peptide_df

  

  janni.roebbecke

  committed
  8a2f243

• clean up

  

  janni.roebbecke

  committed
  2a22e61

• add cleaning of protein groups to evidence import

  

  janni.roebbecke

  committed
  4e7d4a8

• Merge branch 'refs/heads/peptides' into filter-peptides-step

  

  janni.roebbecke

  committed
  f4310f2

• rename

  

  janni.roebbecke

  committed
  f2f198b

• clean Protein IDs for peptide_import and name intensity column Intensity

  

  janni.roebbecke

  committed
  c13c6b5

• implement requested changes: make peptide_df input optional for all preprocessing steps, remove peptide_df input in preprocessing steps, where it is not used

  

  janni.roebbecke

  committed
  c0eb03f

• implement requested changes: make peptide_df input optional for all preprocessing steps, remove peptide_df input in preprocessing steps, where it is not used

  

  janni.roebbecke

  committed
  8a49a7b

Commits on Jun 6, 2024

• unify into one method

  

  janni.roebbecke

  committed
  5a6bcc3

Commits on Jun 7, 2024

• cleanup old names

  

  janni.roebbecke

  committed
  55bb815

• cleanup names

  

  janni.roebbecke

  committed
  7151655

• cleanup names

  

  janni.roebbecke

  committed
  6c74880

• setup form and method

  

  janni.roebbecke

  committed
  b66d342

• small refactor: utilize fill_helper better

  

  janni.roebbecke

  committed
  3f8ea0a

• Merge branch 'refs/heads/filter-peptides-step' into ptm-basic-statistics-amount

  

  janni.roebbecke

  committed
  858dcae

• implemented method

  

  janni.roebbecke

  committed
  b147764

• cleanup rename and docstring

  

  janni.roebbecke

  committed
  01d5bbb

• tests and named sample column from "0" to "Sample"

  

  janni.roebbecke

  committed
  b6a26b5

Commits on Jun 9, 2024

• implemented slow version

  

  janni.roebbecke

  committed
  0812b89

Commits on Jun 11, 2024

• Merge branch 'refs/heads/peptides' into filter-peptides-step

  

  janni.roebbecke

  committed
  107a042

• Merge remote-tracking branch 'refs/remotes/origin/dev' into filter-peptides-step

  

  janni.roebbecke

  committed
  5054c4b

• enable selecting multiple proteins

  

  janni.roebbecke

  committed
  349cc38

• Merge branch 'refs/heads/dev' into filter-peptides-step

  

  janni.roebbecke

  committed
  7cf4f70

Commits on Jun 12, 2024

• Merge branch 'refs/heads/filter-peptides-step' into ptm-basic-statistics-amount

  Show description for 82b7940
  

  janni.roebbecke

  committed
  82b7940

• complete merge

  

  janni.roebbecke

  committed
  639561e

• rename file and fix selecting multiple proteins

  

  janni.roebbecke

  committed
  0f5c4b8

• Merge branch 'refs/heads/filter-peptides-step' into ptm-basic-statistics-amount

  Show description for 8b708d3
  

  janni.roebbecke

  committed
  8b708d3

Commits on Jun 13, 2024

• improve efficiency of methods ptms_per_sample and ptms_per_protein_and_sample

  

  janni.roebbecke

  committed
  e96e9cb

• added test for ptms_per_protein_and_sample

  

  janni.roebbecke

  committed
  962d680

• Merge branch 'refs/heads/dev' into ptm-basic-statistics-amount

  Show description for 037e250
  

  janni.roebbecke

  committed
  037e250

• complete merge (fix testes after merge)

  

  janni.roebbecke

  committed
  abb974b

• cleanup

  

  janni.roebbecke

  committed
  be45b72

• Merge branch 'refs/heads/dev' into ptm-basic-statistics-amount

  Show description for 65bf3b0
  

  janni.roebbecke

  committed
  65bf3b0

Commits on Jun 21, 2024

• implement differential expression with mann-whitney-test on ptm data

  

  janni.roebbecke

  committed
  647e5cd

• implement differential expression with mann-whitney-test on protein data

  

  janni.roebbecke

  committed
  d310234

• refactor input and output handling for Mann-Whitney-test on ptm data

  

  janni.roebbecke

  committed
  8359f90

Commits on Jun 25, 2024

• Merge branch 'refs/heads/dev' into mann-whitney-test

  Show description for a5d4a0b
  

  janni.roebbecke

  committed
  a5d4a0b

• Merge branch 'refs/heads/dev' into mann-whitney-test

  Show description for 7cd0d58
  

  janni.roebbecke

  committed
  7cd0d58

• add additional parameter form user and docstrings

  

  janni.roebbecke

  committed
  c984f37

• fix typo

  

  janni.roebbecke

  committed
  93441fe

• add test for mann whitney on intensity data

  

  janni.roebbecke

  committed
  9d056a4

• add test for mann whitney on ptm data

  

  janni.roebbecke

  committed
  d5194c0

• add mann whitney to volcano plot form

  

  janni.roebbecke

  committed
  a566c24

Commits on Jul 9, 2024

• implement kruskal wallis test on ptm data

  

  janni.roebbecke

  committed
  34f5d03

• implement kruskal wallis test on protein data

  

  janni.roebbecke

  committed
  f875849

• adds tests for kruskal wallis test

  

  janni.roebbecke

  committed
  bb1b032

Commits on Jul 10, 2024

• implement normalization

  

  janni.roebbecke

  committed
  958e3e3

• adapt tests

  

  janni.roebbecke

  committed
  2fe13f9

Commits on Jul 11, 2024

• add unit test for ptm_df normalization

  

  janni.roebbecke

  committed
  2416f3a

• change mock files as to not upset other tests

  

  janni.roebbecke

  committed
  10a1ded

Commits on Jul 16, 2024

• enable volcano plot with ptm data

  

  janni.roebbecke

  committed
  ebfe7b5

Commits on Jul 17, 2024

• make names of select peptides for Protein Step consistent

  

  janni.roebbecke

  committed
  3400951

Commits on Aug 14, 2024

• simplify form and make names more broad

  

  janni.roebbecke

  committed
  1d19007

Commits on Aug 19, 2024

• Merge branch 'refs/heads/normalize-ptm-data' into enable-volcano-plot-with-ptm-data

  

  janni.roebbecke

  committed
  9998014

Commits on Aug 29, 2024

• Names of import section

  

  janni.roebbecke

  committed
  99ca421

Commits on Sep 3, 2024

• Names of import section

  

  janni.roebbecke

  committed
  32c88b0

Commits on Sep 4, 2024

• Add description of Volcano Plot

  

  janni.roebbecke

  committed
  75787a5

Commits on Nov 11, 2024

• Merge branch 'refs/heads/dev' into enable-volcano-plot-with-ptm-data

  Show description for c3e04d1
  

  janni.roebbecke

  committed
  c3e04d1

• complete merge

  

  janni.roebbecke

  committed
  a318c15