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MathOnco
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ploidyEvolution
A general N-compartment model of ploidy states is developed and analyzed.
BSD 2-Clause "Simplified" License
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new crit curve read in
#39
thomasveith
closed
2 years ago
0
Changes to Mathematica and R scripts (LogPlot replaced with Plot, no log transform of Y-axis in 2D boxplots)
#38
thomasveith
closed
2 years ago
0
switch between constant vs. heterogeneous missegregation rates
#37
noemiandor
closed
2 years ago
0
now able to plot various missegregation rates for given population
#36
thomasveith
closed
2 years ago
0
2D boxplot replaced
#35
thomasveith
closed
2 years ago
0
Recent requests on Slack implemented
#34
thomasveith
closed
2 years ago
0
BoundsError encountered for certain spatial input files
#33
noemiandor
opened
2 years ago
1
Add karyotype distribution input from file for initial condition.
#32
gregorykimmel
opened
2 years ago
0
script added for generating 2D boxplots
#31
thomasveith
closed
2 years ago
0
Overhauled toml file for readability. This closes #10, #29
#30
gregorykimmel
closed
2 years ago
0
Create subjects in input file that separate parameter types
#29
gregorykimmel
closed
2 years ago
0
Move all command line arguments except input(output)file and spatial flag to input file
#28
gregorykimmel
closed
2 years ago
0
Path to file with vessel coordinates should be a command line option
#27
noemiandor
closed
2 years ago
0
conservation of cell number incorrect after misseg?
#26
Richard-Beck
closed
2 years ago
2
Merge common parts of ode and spatial models into functions that allow easy modification
#25
gregorykimmel
opened
2 years ago
0
Negative cell concentrations after replating occurs
#24
noemiandor
opened
3 years ago
0
Odd behavior at the boundary of blood vessels
#23
gregorykimmel
closed
3 years ago
0
preallocate birthrates
#22
Richard-Beck
closed
3 years ago
0
Minimal energy needed for growth constraint
#21
gregorykimmel
closed
2 years ago
2
Pdemodel
#20
noemiandor
closed
3 years ago
0
Merge all codebase files into one
#19
gregorykimmel
closed
3 years ago
0
Predicted_LaggingChrPct_TCGA.txt added to data folder
#18
thomasveith
closed
3 years ago
0
Some discrepancies between variable names resolved, plot output improved
#17
thomasveith
closed
3 years ago
0
count to TMP conversion before batch correction
#16
noemiandor
closed
3 years ago
0
Remove minChrom from user control.
#15
gregorykimmel
closed
3 years ago
0
Normalizing raw gene counts to gene length, restrictions on control and sampling
#14
thomasveith
closed
3 years ago
0
Split ploidymovement into two files
#13
gregorykimmel
closed
3 years ago
0
Print out current time point in intervals of a day
#12
gregorykimmel
closed
3 years ago
2
Add save state functionality
#11
gregorykimmel
opened
3 years ago
0
Move options to input file
#10
gregorykimmel
closed
2 years ago
0
Vessel boundary can overlap domain boundary
#9
gregorykimmel
opened
3 years ago
0
distinction between primary and met
#8
noemiandor
closed
3 years ago
0
Now grabbing raw gene counts instead of normalized, added umap output
#7
thomasveith
closed
3 years ago
0
TCGA/GEO data set integration init
#6
thomasveith
closed
3 years ago
0
ODE model not working with default settings
#5
Richard-Beck
closed
3 years ago
0
Calculating normal vectors at vessel boundaries
#4
noemiandor
closed
3 years ago
1
growth rate annotation
#3
noemiandor
closed
3 years ago
1
SingularException during interpolation
#2
noemiandor
opened
3 years ago
1
Noemi
#1
noemiandor
closed
3 years ago
0