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Count-based differential assembly #487

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@hmusta hmusta commented Jun 11, 2024 •
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This adds:

  • Statistical significance tests for differential assembly using binary and count annotations
  • The ability to stream annotation column counts from disk
  • Addition of a disk-streaming row-major integer annotator
  • Complete rewrite of the differential assembly code

@hmusta hmusta mentioned this pull request Jun 11, 2024
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hmusta added 30 commits March 21, 2025 09:54
@hmusta
Merge remote-tracking branch 'origin/master' into count_diff_assem
4460ff9
@hmusta
Merge remote-tracking branch 'origin/master' into count_diff_assem
2d4eb47
@hmusta
switch to new eigen gitlab repo
2cdb25a
@hmusta
unitig test
3b35599
@hmusta
this works
a163692
@hmusta
cleanup
7db5855
@hmusta
more cleanup
678db49
@hmusta
more cleanup
a027455
@hmusta
lots of cleanup
61e3687
@hmusta
fix tests
9fd1544
@hmusta
minor
cfcf098
@hmusta
fix
be4dc72
@hmusta
test
95de5d3
@hmusta
update
dc518bf
@hmusta
updated chi2 pval calculator
b7d061a
@hmusta
fix cutoff
94cad1c
@hmusta
bh
6781f59
@hmusta
fall back to LRT
c1c6e61
@hmusta
test
4846ab4
@hmusta
effect sie
b066ec9
@hmusta
wald test nb
4b9042d
@hmusta
fix eff size
ec20f8a
@hmusta
Merge remote-tracking branch 'origin/master' into count_diff_assem
0d311f1
@hmusta
better nbinom optim and scale values before wald test
f0321d7
@hmusta
minor fix for notest
a4cfa1e
@hmusta
switch to Holm
8ed7c49
@hmusta
Revert "switch to Holm"
71401a4 
This reverts commit 8ed7c49.
@hmusta
simplify
8704ee8
@hmusta
fit nb distribution first, then scale
db81e72
@hmusta
changes
8ec120b
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@hmusta