harrispopgen/mushi

Issues

• alternatives to prox-tv dependency

  #59 opened 3 years ago by wsdewitt
  4

• trend penalty piece of cost functions using incorrect difference order

  #74 opened 3 years ago by wsdewitt
  0

• Question on Ksfs

  #75 opened 3 years ago by RenzoTale88
  2

• Step-by-step guide from mutyper

  #73 opened 3 years ago by RenzoTale88
  2

• write more tests

  #36 opened 4 years ago by wsdewitt
  0

• Accommodate non-uniform time grid in trend filter

  #70 opened 4 years ago by wsdewitt
  0

• update docs after pipeline overhaul

  #67 opened 4 years ago by wsdewitt
  1

• replace total variation / fused lasso with trend filtering

  #57 opened 4 years ago by wsdewitt
  2

• spin out `mushi.optimization` module into an independent package

  #69 opened 4 years ago by wsdewitt
  0

• Tiny bug in pipeline

  #61 opened 4 years ago by terhorst
  1

• `true_divide` error in folded SFS inference with integer SFS data

  #63 opened 4 years ago by wsdewitt
  1

• Folded SFS

  #60 opened 4 years ago by wsdewitt
  1

• duplicate exponent in ridge term

  #58 opened 4 years ago by wsdewitt
  1

• mutyper

  #54 opened 5 years ago by wsdewitt
  0

• Add dvipng to dependencies

  #49 opened 5 years ago by kamdh
  0

• data-dependent Gram-Schmidt orthogonalization

  #51 opened 5 years ago by wsdewitt
  15

• basic sim notebook gone

  #50 opened 5 years ago by kamdh
  0

• test-msprime.ipynb broken

  #30 opened 5 years ago by kamdh
  0

• Notation standardization & improvement

  #43 opened 5 years ago by kamdh
  6

• generalize 3-operator splitting to 4 operators

  #41 opened 5 years ago by wsdewitt
  1

• time calibration

  #40 opened 5 years ago by wsdewitt
  30

• remove stdpopsim submodule

  #44 opened 5 years ago by wsdewitt
  0

• three operator splitting allows negativity

  #37 opened 5 years ago by wsdewitt
  23

• Use "real" coalescent simulation, instead of just the forward model

  #11 opened 5 years ago by wsdewitt
  9

• Convergence theory for large n

  #7 opened 5 years ago by wsdewitt
  5

• Markov random field priors

  #17 opened 5 years ago by wsdewitt
  6

• Get rid of logy, logZ transformation

  #34 opened 5 years ago by kamdh
  2

• Update docs to reflect newest requirements

  #35 opened 5 years ago by kamdh
  0

• test.ipynb broken

  #29 opened 5 years ago by kamdh
  5

• stdpopsim directory empty

  #28 opened 5 years ago by kamdh
  5

• dimension reduction for mutational signatures

  #14 opened 5 years ago by wsdewitt
  0

• ramping regularization with TMRCA CDF

  #16 opened 5 years ago by wsdewitt
  1

• fused lasso

  #13 opened 5 years ago by wsdewitt
  5

• SFS noise model

  #10 opened 5 years ago by wsdewitt
  1

• trapezoidal instead of box quadrature for expected coalescent times

  #2 opened 5 years ago by wsdewitt
  1

• Derive gradient instead of relying on numerical differentiation

  #3 opened 5 years ago by wsdewitt
  10

• Gaussian measure to handle asymptotic boundary condition

  #4 opened 6 years ago by wsdewitt
  1

• Enforcing flatness beyond the coalescent horizon

  #8 opened 6 years ago by wsdewitt
  14

• Get rid of shitty xkcd plots

  #9 opened 6 years ago by kamdh
  0

• indexing errors in formulae

  #5 opened 6 years ago by kamdh
  4

• enforcing eta(T) = eta(infty)

  #6 opened 6 years ago by kamdh
  1

• push code commit

  #1 opened 6 years ago by kamdh
  0