bioIOT 0.2.2
- CRAN review fixes: removed single quotes around non-software terms
in the DESCRIPTION; no more
T/F variable names
(the observed transitions argument T of
fit_iot() and row_ce_loss() is now
T_obs, and the fitted feature count F is now
n_feat); the has_cel_file() /
find_platform_file() example is now runnable (no
\dontrun).
bioIOT 0.2.1
- Documentation and metadata fixes.
bioIOT 0.2.0
- New R core solver:
soft_sinkhorn()
(Anderson-accelerated semi-relaxed soft Sinkhorn),
row_conditional(), make_cost(),
row_ce_loss(), zscore_phi().
- New fitting:
fit_iot() with exact implicit gradients,
two-stage debias refit and multi-restart;
print/summary methods for
bioIOT_fit.
- New trajectory layer:
transition_matrix(),
pseudotime_from_transition(),
build_state_features().
- New single-cell interfaces:
runIOT() generic with
matrix, SingleCellExperiment and Seurat methods.
- New visualisation (ggplot2):
plot_transition_heatmap(),
plot_transition_flow(), plot_theta(),
plot_pathway_trend().
- New reproducible demo:
simulate_iot_states() plus
bundled dataset demo_iot_states.
- New vignette and expanded test suite (implicit-gradient vs finite
differences, recovery, interfaces, plots).
bioIOT 0.1.0
- Initial release:
pathway_markers,
score_pathways, collapse_probes,
gsm_id, has_cel_file,
find_platform_file.