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47a092f
Adding metabolomics filtering feature
feliciaschulz Sep 29, 2025
5691200
Metabolomics example data set
feliciaschulz Sep 29, 2025
5b11795
Adding test for metabolomics filtering function
feliciaschulz Sep 29, 2025
e03aa2e
Filter functions added.
feliciaschulz Sep 29, 2025
81f328d
Updating and cleaning up filtering docstrings
feliciaschulz Oct 13, 2025
4d70e02
Filtering example api jupyter notebook added.
feliciaschulz Oct 13, 2025
53a5419
Changed filtering function name.
feliciaschulz Oct 13, 2025
a15008a
✨ Feat: Add script and docs for QC-based LOESS drift correction module
feliciaschulz Nov 17, 2025
8461b74
✏️ Fix: prevent division by zero, edit documentation
feliciaschulz Jan 30, 2026
50ce9d6
Adding metabolomics example data for drift correction function testing
feliciaschulz Jan 30, 2026
6f2e911
Editing example aradopsis metabolomics data (removing faulty row).
feliciaschulz Feb 2, 2026
a41d621
📝 Adding api example notebook for drift correction
feliciaschulz Feb 2, 2026
8d5e6a7
Adding jupytext file for drift correction api example.
feliciaschulz Feb 2, 2026
c0c5933
:sparkles: Start collecting dataframe schemas for input and output Da…
enryH Oct 10, 2025
bd7014c
:sparkles: custom PR template for new module (#39)
enryH Oct 24, 2025
d7ca8c4
🔧 Update CI (#45)
enryH Dec 2, 2025
67c0e31
:truck: separate batch correction from normalization (#46)
enryH Jan 12, 2026
95cd161
Documentation updates (#47)
enryH Jan 12, 2026
acf179e
:art: consistent scaling and naming (#48)
enryH Jan 14, 2026
2bb6946
:memo: add Contributing.md as reference to PR template (#49)
enryH Jan 19, 2026
c2110c5
Metabolomics example data (#50)
enryH Jan 19, 2026
0064f58
Adding function for visualising example of the LOESS drift correction.
feliciaschulz Apr 29, 2026
8829a54
Adding functions for alternative drift correction method: CPCA
feliciaschulz May 1, 2026
256b99c
Adding CPCA drift correction to api examples and refining code.
feliciaschulz May 1, 2026
08b7b4c
Adding example data for metabolomics
feliciaschulz May 1, 2026
cd06c47
Creating jupytext file for drift correction api example
feliciaschulz May 4, 2026
650fd6e
Merge remote-tracking branch 'origin/main' into drift-correction
feliciaschulz May 4, 2026
7772ec6
:art: format tutorials and code (black and isort)
feliciaschulz May 4, 2026
e132333
:art: apply ruff suggestions
feliciaschulz May 4, 2026
fba0e7f
Merge branch 'main' into drift-correction
enryH May 5, 2026
4b0b5b9
docs: update markdown reference
github-actions[bot] May 5, 2026
8963030
:art: Updating index.md to add drift correction api example.
feliciaschulz May 4, 2026
543bdfc
:art: put drift correction plotting functions from src to api examples
feliciaschulz May 11, 2026
ee59986
:art: implement logger in drift correction functions to replace print…
feliciaschulz May 11, 2026
98c8fbe
remove excel lock file
feliciaschulz May 12, 2026
4904948
adding synced jupytext drift_correction.py
feliciaschulz May 12, 2026
4eda2f9
Changing import order for ruff checks
feliciaschulz May 12, 2026
10a8a03
docs: update markdown reference
github-actions[bot] May 12, 2026
ec07a78
:art: removing unused imports
feliciaschulz May 12, 2026
1b2acee
:art: Typo in documentation
feliciaschulz May 12, 2026
d4a136b
:art: Typo in documentation
feliciaschulz May 12, 2026
7961ade
:art: Typo in documentation
feliciaschulz May 12, 2026
6adf32c
:art: fixing error in documentation
feliciaschulz May 12, 2026
b74e9ed
docs: update markdown reference
github-actions[bot] May 12, 2026
a78728e
:art: ensuring x_qc is sorted so CubicSpline works correctly
feliciaschulz May 12, 2026
436f3e7
:art: fixing linting errors from ruff
feliciaschulz May 12, 2026
f5b9005
:art: filtering issue: opposite functionality to what the documentati…
feliciaschulz May 12, 2026
974acb6
docs: update markdown reference
github-actions[bot] May 12, 2026
c14a15f
:art: implementing changes suggested by copilot: NaN value handling, …
feliciaschulz May 12, 2026
f62df20
:art: isort on multiple files to improve order of inputs.
feliciaschulz May 12, 2026
a086b96
:art: format notebooks a bit more and add filtering to index
enryH May 19, 2026
2146c39
:art: clear outputs and hide installation panel output
enryH May 21, 2026
b5244ce
:art: remove unnamed column on integer indices in display
enryH May 22, 2026
f23aa9e
:art: Changing example data for loess-based drift correction api exam…
feliciaschulz May 22, 2026
8050ee6
:art: fixing black errors
feliciaschulz May 22, 2026
ccb6b67
:art: improvements in visibility
enryH May 26, 2026
39d4aff
:bug: set defaults for parameters
enryH May 26, 2026
0679cde
docs: update markdown reference
github-actions[bot] May 26, 2026
29fbb65
:art: saveguard string and switch to logging
enryH May 26, 2026
f5fbae7
:art: format
enryH May 26, 2026
191249b
:bug: remove outdated parameter from call
enryH May 26, 2026
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40 changes: 20 additions & 20 deletions docs/api_examples/batch_correction.ipynb
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "markdown",
"id": "27b8d53e",
"id": "2b2c0d3a",
"metadata": {
"lines_to_next_cell": 2
},
Expand All @@ -19,7 +19,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "dcc1505c",
"id": "e452352c",
"metadata": {
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"hide-output"
Expand All @@ -33,7 +33,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "563697dc",
"id": "c7399c16",
"metadata": {
"tags": [
"hide-input"
Expand Down Expand Up @@ -107,7 +107,7 @@
},
{
"cell_type": "markdown",
"id": "60ee225e",
"id": "cd6853a6",
"metadata": {},
"source": [
"\n",
Expand All @@ -117,7 +117,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "a32698b4",
"id": "cf489def",
"metadata": {
"tags": [
"parameters"
Expand All @@ -141,7 +141,7 @@
},
{
"cell_type": "markdown",
"id": "9bd7687c",
"id": "14907bce",
"metadata": {},
"source": [
"## Data loading\n",
Expand All @@ -151,7 +151,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "ced30460",
"id": "fde7c5dd",
"metadata": {
"tags": [
"hide-input"
Expand All @@ -169,7 +169,7 @@
},
{
"cell_type": "markdown",
"id": "55b42bc2",
"id": "2113619e",
"metadata": {},
"source": [
"Metadata here is of type integer. All floats are proteomics measurements."
Expand All @@ -178,7 +178,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "857b0522",
"id": "afd00cfd",
"metadata": {
"tags": [
"hide-input"
Expand All @@ -192,7 +192,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "23657991",
"id": "29a05170",
"metadata": {
"tags": [
"hide-input"
Expand All @@ -206,7 +206,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "8bef0df5",
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"metadata": {},
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"source": [
Expand All @@ -216,7 +216,7 @@
},
{
"cell_type": "markdown",
"id": "713a7b35",
"id": "7bf84ee6",
"metadata": {},
"source": [
"## Before batch correction\n",
Expand All @@ -226,7 +226,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "986f7cab",
"id": "0b0c854c",
"metadata": {
"tags": [
"hide-input"
Expand All @@ -242,7 +242,7 @@
},
{
"cell_type": "markdown",
"id": "2bf8ca74",
"id": "426ee866",
"metadata": {
"lines_to_next_cell": 0
},
Expand All @@ -258,7 +258,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "1cf6f58b",
"id": "f9ba51bd",
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -273,7 +273,7 @@
},
{
"cell_type": "markdown",
"id": "ca46af9e",
"id": "1aa67514",
"metadata": {},
"source": [
"Plot PCA and UMAP after batch correction on standard normalized data"
Expand All @@ -282,7 +282,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "cdc4afa2",
"id": "907ed6c7",
"metadata": {
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Expand All @@ -296,7 +296,7 @@
},
{
"cell_type": "markdown",
"id": "9fda9a50",
"id": "a530c6ba",
"metadata": {},
"source": [
"See change by substracting combat corrected data from original data.\n",
Expand All @@ -306,7 +306,7 @@
{
"cell_type": "code",
"execution_count": null,
"id": "e9cecdd8",
"id": "88ab0d76",
"metadata": {
"tags": [
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Expand All @@ -319,7 +319,7 @@
},
{
"cell_type": "markdown",
"id": "d27e6f10",
"id": "84ad3f0d",
"metadata": {},
"source": [
"Done."
Expand Down
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