Commits · d17cab67c9bed4054e7d69f30249d2dda895a303 · github_fork / Presto 20250701

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Jul 27, 2020
- fixed nested contrasts in make contrast mat · d17cab67
  Ilya Korsunsky authored Jul 27, 2020
  
  d17cab67
Jul 25, 2020
- typo · f47c313c
  Ilya Korsunsky authored Jul 24, 2020
  
  f47c313c
- typo · 61853070
  Ilya Korsunsky authored Jul 24, 2020
  
  61853070
- export fxns · f5d0504e
  Ilya Korsunsky authored Jul 24, 2020
  
  f5d0504e
- Merge branch 'glmm' of https://github.com/immunogenomics/presto into glmm · ac17d381
  Ilya Korsunsky authored Jul 24, 2020
  
  ac17d381
- functions for contrasts and covariance · 7658c327
  Ilya Korsunsky authored Jul 24, 2020
  
  7658c327
Jul 10, 2020
- changed p value computation to be in log space, to handle more extreme values · 8da49317
  ilyakorsunsky authored Jul 09, 2020
  
  8da49317
Jul 03, 2020
- in correct_counts, specify exact levels to remove · 968ecbbc
  ilyakorsunsky authored Jul 02, 2020
  
  968ecbbc
Jul 02, 2020
- fized bug in glmm_internal.R · 8ec89c2f
  Ilya Korsunsky authored Jul 02, 2020
  
  8ec89c2f
- Merge branch 'glmm' of https://github.com/immunogenomics/presto into glmm · 825eb6e2
  Ilya Korsunsky authored Jul 02, 2020
  
  825eb6e2
- Removed rowwise operations, they are super slow · 65d4fd86
  ilyakorsunsky authored Jul 02, 2020
  
  65d4fd86
- removed rowwise operations, they are very slow · 0a25fe8b
  Ilya Korsunsky authored Jul 02, 2020
  
  0a25fe8b
- ungroup rowwise in .merge_betas and .merge_sigmas · c92d94fa
  ilyakorsunsky authored Jul 01, 2020
  
  c92d94fa
Jun 13, 2020
- added patch to .ncore · a6bffff2
  Ilya Korsunsky authored Jun 12, 2020
  
  a6bffff2
- moved parallel functions from furrr future_map directly to futures · 0947a2f2
  Ilya Korsunsky authored Jun 12, 2020
  
  0947a2f2
Jun 12, 2020
- augmented effects.presto to summarize effects over multiple (potentially) nested variables · 69131e39
  Ilya Korsunsky authored Jun 11, 2020
  
  69131e39
Apr 30, 2020
- fixed correct_counts function · dc3a6ebe
  Ilya Korsunsky authored Apr 30, 2020
  
  dc3a6ebe
Apr 29, 2020
- removed extra lines · 634c5ff4
  Ilya Korsunsky authored Apr 29, 2020
  
  634c5ff4
- bugs etc. · 69f31345
  Ilya Korsunsky authored Apr 29, 2020
  
  69f31345
- more functions to glmm · 6a10424b
  Ilya Korsunsky authored Apr 28, 2020
  
  6a10424b
Apr 28, 2020
- fixed bug, removed documentation for old functions · 5a49ba81
  Ilya Korsunsky authored Apr 28, 2020
  
  5a49ba81
- first commit of functions for cached lme4 matrix results and analyses · 594a67fb
  Ilya Korsunsky authored Apr 27, 2020
  
  594a67fb
Apr 24, 2020
- fixed treatment of adding back residuals in regress_out_one_gene · 16bc0d7c
  Ilya Korsunsky authored Apr 23, 2020
  
  16bc0d7c
Apr 22, 2020
- add back residuals to poisson predicted values · 910b8669
  Ilya Korsunsky authored Apr 22, 2020
  
  910b8669
- fixed bug in glmm.R · ab45bb97
  Ilya Korsunsky authored Apr 21, 2020
  
  ab45bb97
- functions to regress out random effects · fa5c85e1
  Ilya Korsunsky authored Apr 21, 2020
  
  fa5c85e1
Apr 20, 2020
- error checking, try again · 8b75e461
  Ilya Korsunsky authored Apr 20, 2020
  
  8b75e461
- error catching for when glmer fails · 8e72f6f4
  Ilya Korsunsky authored Apr 20, 2020
  
  8e72f6f4
- fixed some bugs · 6b129f99
  Ilya Korsunsky authored Apr 20, 2020
  
  6b129f99
- initial commit of lme4 DGE models and meta analysis functions · b1a09bdd
  Ilya Korsunsky authored Apr 20, 2020
  
  b1a09bdd
Feb 25, 2020
- allow sum and mean collapsing · 7f63f960
  Ilya Korsunsky authored Feb 24, 2020
  
  7f63f960
Nov 19, 2019
- added params to within · 3e31a977
  Ilya Korsunsky authored Nov 18, 2019
  
  3e31a977
Nov 17, 2019
- within analysis · 0f167bff
  Ilya Korsunsky authored Nov 16, 2019
  
  0f167bff
- added options to do DGE within clusters · 156062bc
  Ilya Korsunsky authored Nov 16, 2019
  
  156062bc
Nov 16, 2019
- filter genes locally in the pairwise analysis · b5a71b4f
  Ilya Korsunsky authored Nov 15, 2019
  
  b5a71b4f
- filter genes locally in the pairwise analysis · de9b094a
  Ilya Korsunsky authored Nov 15, 2019
  
  de9b094a
Nov 15, 2019
- added keep_n option to collapse counts · dfde6966
  Ilya Korsunsky authored Nov 14, 2019
  
  dfde6966
Nov 13, 2019
- fixed code in pseudobulk.R · 09036560
  Ilya Korsunsky authored Nov 13, 2019
  
  09036560
Nov 09, 2019
- added min_cells_per_group to collapse counts function · 303ea288
  Ilya Korsunsky authored Nov 08, 2019
  
  303ea288
- added functions to do pairwise group comparisons · ad54ceab
  Ilya Korsunsky authored Nov 08, 2019
  
  ad54ceab

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Commits · d17cab67c9bed4054e7d69f30249d2dda895a303