0.10.4 (2026-05-04)
- Set reporter (genomic) varints empty ref/alt allele to 0 (3c39029)
0.10.3 (2026-03-05)
- replace None with pd.NA in MPRAData allele processing for improv… (1c724b2)
- replace None with pd.NA in MPRAData allele processing for improved compatibility (8ec5372)
0.10.2 (2026-03-04)
0.10.1 (2026-03-03)
0.10.0 (2026-03-02)
- modification of normalization (over total counts not average per barcode per oligo) (#87)
0.9.1 (2026-01-08)
- overview update (83bb09e)
- quickstart and other improvements (66a2771)
- update quictstart and minor other updates (36622f7)
- Zenodo link and documentation update (5e4c62d)
0.9.0 (2025-09-16)
- Renames cli sequence_design to combine (#79)
- Some othere CLI commands changed (#75)
- Normalization only done on raw or sampled counts. Var filter (barcode filter) not used (#78)
- validate empty files as invalid (1fddaeb)
- Normalization only done on raw or sampled counts. Var filter (barcode filter) not used (#78)
- Outlier detection is now in line with the manuscript (#75)
0.8.2 (2025-07-01)
- improved cli get reporter genomic elements/variants (044b2a5)
- chromosome maps with X and Y (0becc21)
- chromosome_map can distiguish between hg19 and hg38 (dd8afe5)
0.8.1 (2025-06-27)
0.8.0 (2025-06-27)
- loading chro map files in source. requires python 3.9+ (#67)
0.7.4 (2025-06-26)
0.7.3 (2025-06-17)
- BC counts per oligo where not dropped and therefor enot recomputed after (down) sampling (#63) (d615251)
0.7.2 (2025-06-12)
- better API documentation on readthedocs (d289a4c)
0.7.1 (2025-06-11)
- readthedocs documentation inkluding API (22023bd)
0.7.0 (2025-06-04)
- MPRAlib is now always in lowercase (also on pypi)
- minimum required anndata 0.11.3 (7d56652)
- Python compatibility 3.8+ compatibility using Optional for typing. (7649bc9)
- update docs for lowercase (0631f7c)
- MPRAlib is now always in lowercase (also on pypi) (0b6108a)
0.6.5 (2025-06-03)
- complexity estimates on barcode level (06a2173)
0.6.4 (2025-05-28)
- validate files. empty ref/alt allele for variant files must be 0 (391703a)
0.6.3 (2025-05-23)
- sampling was buggy (abe540b)
0.6.2 (2025-05-22)
- cli to validate standardized file formats for MPRA using json schema (a078ad9)
- coverage report and automatic tests using github actions (d8139b6)
0.6.1 (2025-04-09)
- SyntaxError: EOL while scanning string literal (11ce617)
- correct colab path (8fbeb16)
- example data (79cdae9)
- updated mpralib notebook (c1f53be)
- updated python notebooks (83fdfc4)
0.6.0 (2025-04-03)
- barcode_counts is now part available in MPRAdata as layer
- barcode_counts is now part available in MPRAdata as layer (c9b04ec)
0.5.0 (2025-04-01)
- gobal variant map. Now metadata is called "sequence design"
- dna_vs_rna and barcodes per oligo plots.
- correlation plot. breaks corrrelation due to new count type enum
- new utils sub library
- correlation plot. breaks corrrelation due to new count type enum (f0e46a1)
- dna_vs_rna and barcodes per oligo plots. (3430538)
- gobal variant map. Now metadata is called "sequence design" (2743e20)
- normalized counts in output files (8526f9f)
- outlier plot (17cf8d1)
- pairwise correlation plots (bd1d118)
- plot functionality (b789c41)
- bcalm and mpralm element scripts with empty rows (Not observed) (174657b)
- reporter genomic variant or element (b250470)
- new utils sub library (323e319)
0.4.0 (2025-03-21)
- the whole code
- the whole code (6f2f2b7)
- add filtering options for elements and variants in get_counts function (971986b)
- full cli functionality (6f2f2b7)
- broken cli methods (8386f83)
0.3.0 (2025-03-04)
- splitting oligo and barcode counts resulting in different interface
- adding qc metric notebook (ab17436)
- qc metric update (eda4ca4)
- splitting oligo and barcode counts resulting in different interface (ef09d7a)
0.2.2 (2025-02-27)
- initialize barcode_threshold when it is not there (4f09174)
0.2.1 (2025-02-27)
- adding rna and dna counts correlations (b2b4d60)
0.2.0 (2025-02-21)
- implemented count sampling
- Control pseudo counts (0534bb6), closes #14
- implement RNA and DNA count methods with sampling and filtering (95e3be9)
- implemented count sampling (bfa4da5)
- utils method for barcode output format (#20) (81273de), closes #15
- issues and prepare to split up counts (484d936)
- add chromosome mapping utility and data files for hg19 and hg38 (f037b92)
- add MPRA analysis script and enhance MPRAdata class with variant mapping and counts (00de9c0)
- add MPRA element analysis script and enhance MPRAdata class with element DNA and RNA counts (df5e5fe)
- add output option for MPRA data object and enhance element and variant reporting functions (4a81736)
- random sampling of barcodes (62330d0)
- adjust YAML linter configuration for comments spacing (ab6c18f)