--- a
+++ b/CHANGELOG.md
@@ -0,0 +1,137 @@
+# InMoose release changelog
+
+## [0.7.4-dev]
+
+- fix single sample clustering error, changing cluster consensus to nan
+- improve pyDESeq2 documentation 
+
+## [0.7.3]
+
+- fix dispersion estimation and MAD computation in `deseq2` module
+- improve GLM fit in `deseq2` module
+- create `cohort_qc` module with `CohortMetric` and `QCReport` classes to
+  evaluate dataset quality after batch effect correction
+- improve `cohort_qc` module when the number of covariates is 0 or 1
+- improve documentation for `diffexp` module
+- improve documentation for `consensus_clustering` module
+- batch effect correction functions now accept `AnnData` as input
+- fix p-value adjustment in `deseq2` module
+- add logos and badges in the README
+
+## [0.7.2]
+
+- opt out of `numpy` 2.1.0 until `statsmodels` supports it
+- fix an array indexing bug in function `meta_de`
+- function `meta_de` is now robust to NaN *p*-values
+- allow arbitrary types for `batch` and `group` arguments in function
+  `sim_rnaseq`
+
+## [0.7.1]
+
+- fix a bug when splicing a `DEResults`
+- fix coverage report upload in CI/CD pipeline
+- improve documentation landing page and references
+- use a package-specific logger
+
+## [0.7.0]
+
+- harmonize differential expression analysis results across `deseq2`, `edgepy`
+  and `limma` modules
+- add a meta-analysis feature for differential expression
+
+## [0.6.0]
+
+- move most of C++ code to Python and Cython
+- compatibility with `numpy` 2.0.0
+
+## [0.5.1]
+
+- fix pycombat covariates action remove with count dataframe output
+
+## [0.5.0]
+
+- add experimental support for MSVC compiler
+- add R-like functions for fitting linear models in module `utils`
+- add a function to compute natural cubic spines basis in module `utils`
+- add tmixture functions from R package limma
+- add linear model fit functions from R package limma
+- add functions handling duplicated probes from R package limma
+- lint code with `ruff`
+- add a "differential expression analysis" section to the doc
+
+## [0.4.1]
+
+- fix an incorrect github action version number
+
+## [0.4.0]
+
+- support for Python 3.12
+- bump github actions versions
+- publish coverage report to coveralls.io
+- port `edgeR` functions for differential expression to `inmoose`
+- Modifiy clustering stability plot
+- remove many (not all) warnings
+
+## [0.3.1]
+
+- Fix issue #25 and #10 related to counts parameter data format check and gestion (when it's a pandas dataframe)
+- add DESeq2 variance stabilizing transformation to the `deseq2` package
+- improve the error message for confounding variable in `pycombat` package
+- fix build on readthedocs
+
+## [0.3.0]
+
+- add and optimize a few functions in the `utils.stats` module
+- add a module featuring a port of the DESeq2 R package
+
+## [0.2.4]
+
+- add a `data` module, with two RNA-Seq datasets: `pasilla` and `airway`
+- fix build on readthedocs
+- updated bibliography with our BMC Bioinformatics paper
+- add verbose to consensus clustering computation
+- add a utility class `VirtualCohortInput` to better check the well definition
+  of inputs to the batch effect correction routines
+
+## [0.2.3]
+
+- fix syntax-impairing typos in `pyproject.toml`
+
+## [0.2.2]
+
+- proper documentation for the `sim` module
+- code is now formatted with `black`
+- add a link to the documentation in the README file
+- better handling of covariates in `pycombat` module
+
+## [0.2.1]
+
+- add a function to generate simulated RNA-Seq and scRNA-Seq data
+- drop support of Python 3.8 due to memory management issues in extensions
+- add a module to perform consensus clustering and select the optimal number of
+  clusters
+
+## [0.2.0]
+
+- `inmoose` now requires Python >= 3.8
+- reorganize tests directory
+- refactor module for batch effect correction. It is now named `pycombat`
+  (instead of `batch`), and the function to correct batch effect on microarray
+  data is now `pycombat_norm` (instead of `pycombat`).
+- refactor design matrix computation, to share the code between `pycombat_norm`
+  and `pycombat_seq`
+- batch effect correction functions now accept both `numpy` arrays and `pandas`
+  dataframes as input for the counts matrix
+- improved logging: no more `print`s, better log formatting
+- `inmoose` doc is now on `readthedocs.org`
+
+## [0.1.1]
+
+- upgrade to Cython 3.0.0b2
+- fix C++ extension loading on Linux
+- add CI/CD to build, test and publish distributions
+
+## [0.1.0]
+
+Initial release
+