8000 Commits · cantinilab/Circe · GitHub

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Commits on Jun 25, 2025

Bump to version 0.3.8 !
r-trimbour
committed
Bump to version 0.3.8 !
r-trimbour
committed
Update setup.py
r-trimbour
authored
Bump to version 0.3.8 !
r-trimbour
committed

Commits on Jun 24, 2025

added attrs dependency to match potential pybiomart installations
r-trimbour
committed
add warning on non expressed peaks in metacell computation
r-trimbour
committed
reorganised dependencies
r-trimbour
committed
reorganised dependencies
r-trimbour
committed
using progress.track to display preparation of random DNA windows
r-trimbour
committed
using track instead of progess ; solves mutlithreading error
r-trimbour
committed
using track instead of progess ; solves mutlithreading error
r-trimbour
committed
remove heartbeat setting for workers
r-trimbour
committed
remove the copy when handling dense matrices in _remove_null_rows
r-trimbour
committed
increase heart beat for workers in the calcul of alpha
r-trimbour
committed
use rich to plot de window sampling
r-trimbour
committed

Commits on Jun 23, 2025

reduce to only n_samples windows selected once filtering is done ; added chromosomes_sizes parameter
r-trimbour
committed
reduce to only n_samples windows selected once filtering is done ; added chromosomes_sizes parameter
r-trimbour
committed
reduce to only n_samples windows selected once filtering is done ; added chromosomes_sizes parameter
r-trimbour
committed
reduce to only n_samples windows selected once filtering is done ; added chromosomes_sizes parameter
r-trimbour
committed
reduce to only n_samples windows selected once filtering is done ; added chromosomes_sizes parameter
r-trimbour
committed

Commits on Jun 22, 2025

removed dask cluster around sliding_graphical_lasso parallelisation, back to parallelisation per chromosome
r-trimbour
committed
removed dask cluster around sliding_graphical_lasso parallelisation, back to parallelisation per chromosome
r-trimbour
committed
removed dask cluster around sliding_graphical_lasso parallelisation, back to parallelisation per chromosome
r-trimbour
committed
removed dask cluster around sliding_graphical_lasso parallelisation, back to parallelisation per chromosome
r-trimbour
committed

Commits on Jun 21, 2025

intorduce cov_with_appended_zeros to calculate then correct the cov from the non _all-zero observations (numerous in scATAC)
r-trimbour
committed
filtering out cells at 0 in each windows
r-trimbour
committed
filtering out cells at 0 in each windows
r-trimbour
committed
filtering out cells at 0 in each windows
r-trimbour
committed
client in average_alapha: increased timeout
r-trimbour
committed
client in average_alapha: increased timeout
r-trimbour
committed
client in average_alapha: increased timeout
r-trimbour
committed
use a context-manager fof the client of average_alpha
r-trimbour
committed

Commits on Jun 20, 2025

remove unnecessary prints
r-trimbour
committed
fixed tests for danse anndata.X
r-trimbour
committed
fixed tests for danse anndata.X
r-trimbour
committed

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