Closed rcannood closed 4 years ago
Implement knockdown / knockouts / overexpression experiments.
Implement better single-cell regulatory activity by determining the effect on propensity values after knocking out a transcription factor.
Implement adding noise to the kinetic params of individual simulations.
Kinetics (transcription rate, translation rate, decay rate, ...) are based on Schwannhausser et al. 2011.
Changed many parameter names to better explain its purpose.
Fix module naming of backbones derived from backbone_branching().
backbone_branching()
Allow to plot labels in plot_simulation_expression().
plot_simulation_expression()
Improve backbone_disconnected() and backbone_converging().
backbone_disconnected()
backbone_converging()
Rename required columns in backbone() input data.
backbone()
Use backbone_linear() to make backbone_cyclic() randomised.
backbone_linear()
backbone_cyclic()
Added a decay rate for pre-mRNAs as well.
Kinetics: redefine the decay rates in terms of the half-life of these molecules.
Only compute dimred if desired.
Allow computing the propensity ratios as ground-truth for rna velocity.
Implement fix for double positives in bblego backbones.
bblego
Fix graph plotting mixup of interaction effects (up/down).
Made a fix to the computation of feature_info$max_protein.
feature_info$max_protein
NEW FEATURES:
Implement knockdown / knockouts / overexpression experiments.
Implement better single-cell regulatory activity by determining the effect on propensity values after knocking out a transcription factor.
Implement adding noise to the kinetic params of individual simulations.
Kinetics (transcription rate, translation rate, decay rate, ...) are based on Schwannhausser et al. 2011.
Changed many parameter names to better explain its purpose.
MINOR CHANGES:
Fix module naming of backbones derived from
backbone_branching().Allow to plot labels in
plot_simulation_expression().Improve
backbone_disconnected()andbackbone_converging().Rename required columns in
backbone()input data.Use
backbone_linear()to makebackbone_cyclic()randomised.Added a decay rate for pre-mRNAs as well.
Kinetics: redefine the decay rates in terms of the half-life of these molecules.
Only compute dimred if desired.
Allow computing the propensity ratios as ground-truth for rna velocity.
BUG FIXES:
Implement fix for double positives in
bblegobackbones.Fix graph plotting mixup of interaction effects (up/down).
Made a fix to the computation of
feature_info$max_protein.