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Remove zFPKM #245

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Merged
JoshLoecker merged 28 commits into from
Feb 10, 2026
Merged

Remove zFPKM #245

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346f794
fix(fpkm): update imports for zFPKM calculation improvements
JoshLoecker Feb 9, 2026
985c6f2
fix(fpkm): use Salmon quantification instead of STAR quantification
JoshLoecker Feb 9, 2026
d350063
chore: ruff formatting
JoshLoecker Feb 9, 2026
7482250
chore: fill with integers for faster processing
JoshLoecker Feb 9, 2026
155c822
chore: remove unnecessary async function usage
JoshLoecker Feb 9, 2026
f7b3a06
fix: remove non existant genes from conversion
JoshLoecker Feb 9, 2026
0e4a2c3
refactor: use more explicit (albeit longer) code to create gene_info …
JoshLoecker Feb 9, 2026
ab66599
chore: import required modules
JoshLoecker Feb 9, 2026
95654b3
refactor: optional argument for fragment data
JoshLoecker Feb 9, 2026
dec37b0
refactor: improve handling for single cell data
JoshLoecker Feb 9, 2026
fc1d45f
chore: generalize data type input
JoshLoecker Feb 9, 2026
e1505d1
chore: ruff formatting
JoshLoecker Feb 9, 2026
849ba2e
chore: simplify FPKM/RPKM calculations; properly compute per-gene FPK…
JoshLoecker Feb 9, 2026
3234413
refactor: move zfpkm calculation to external package
JoshLoecker Feb 9, 2026
f90c388
chore: use np.bool for boolean array
JoshLoecker Feb 9, 2026
8253a7d
chore: ruff formatting
JoshLoecker Feb 9, 2026
c52d2e8
feat: allow setting negative zFPKM results to 0
JoshLoecker Feb 9, 2026
e2e6350
feat: simplification to use external zfpkm package
JoshLoecker Feb 9, 2026
2ad9887
feat: allow providing the fragment size filepath (from rnaseq preproc…
JoshLoecker Feb 9, 2026
6af3990
chore(ruff): reduce max line length
JoshLoecker Feb 9, 2026
479fce2
chore(ruff): mark unsorted imports as fixable
JoshLoecker Feb 9, 2026
d83e974
chore(uv): lock pyproject file
JoshLoecker Feb 9, 2026
1df385c
chore: remove zfpkm related code as it is now an external package
JoshLoecker Feb 9, 2026
eed2c93
revert: remove local pyproject requirement
JoshLoecker Feb 9, 2026
fa54bc7
chore: remove zfpkm testing files
JoshLoecker Feb 9, 2026
990490d
Merge branch 'develop' into remove-zfpkm
JoshLoecker Feb 10, 2026
eb9a551
chore: force sync lock
JoshLoecker Feb 10, 2026
e7c5c11
Purge `fast_bioservices` (#246)
JoshLoecker Feb 10, 2026
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333 changes: 0 additions & 333 deletions main/como/approx.py
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