Skip to content
Open
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
30 commits
Select commit Hold shift + click to select a range
6bc7488
Propagate Nunique column and minor fixes
stephaniesamm Apr 29, 2026
41c8d95
Fix off by one sort bug for make negs
stephaniesamm Apr 30, 2026
25b3198
Cluster unique genes using integer IDs and lookup-based map-back.
stephaniesamm May 8, 2026
0515d44
Minor fixes for consistency with original code
stephaniesamm May 8, 2026
fa5dff2
Refactor cluster ID mapping using pandas map().
stephaniesamm May 8, 2026
0232b32
First draft of cutoff selection experiment.
stephaniesamm May 11, 2026
87aec01
Extracted sort to bash script for common use by cutoff experiment.
stephaniesamm May 11, 2026
2cb6b59
Reuse code; clean up; test run on Klimentova.
stephaniesamm May 11, 2026
0029e1a
Ran cut off selection experiment on Hejret & Manakov.
stephaniesamm May 12, 2026
82ac785
Including list of neg sampling block labels of failing blocks in summ…
stephaniesamm May 12, 2026
d57cb27
Added failing mir-17 block analysis for Manakov_remaining.
stephaniesamm May 14, 2026
4bd18fb
Reran updated downstream utility script on Hejret & Klimentova.
stephaniesamm May 14, 2026
d605af4
Restructured failing family analysis; added README for entire cutoff_…
stephaniesamm May 14, 2026
fbb5e35
Updated make_neg_sets to randomly drop excess positives for which ins…
stephaniesamm May 14, 2026
1fe3672
Updated README.
stephaniesamm May 14, 2026
7079806
Added genomic annotator.
stephaniesamm May 18, 2026
cef6695
Reordered post process pipeline steps to annotate only positives, sav…
stephaniesamm May 21, 2026
71c8893
Fixed genomic annotator to handle strand; updated git commit.
stephaniesamm May 22, 2026
cf65890
Added filtering of genomic annotator output for selected cols.
stephaniesamm May 22, 2026
fb81738
Updated make negs to account for new cols.
stephaniesamm May 22, 2026
94b894a
Updated README.
stephaniesamm May 22, 2026
6cb2469
Updated documentation.
stephaniesamm May 22, 2026
1686737
Make postprocess scripts location-independent; unify step numbers acr…
stephaniesamm May 22, 2026
1e4cc8f
Added master script to run pipeline; updated genomic annotator instal…
stephaniesamm May 22, 2026
480f324
Refactored to handle running in cohort or single dset mode.
stephaniesamm Jun 2, 2026
3b8ab35
Fixed transcript coordinates to integers not float.
stephaniesamm Jun 3, 2026
0c2d363
Fixed mixed dtypes in cluster IDs bug causing production of gene,nonc…
stephaniesamm Jun 3, 2026
01c9db0
Updated cutoff selection analysis; different dtypes was already handl…
stephaniesamm Jun 3, 2026
7cecc23
Keep all candidate miRNA names.
stephaniesamm Jun 4, 2026
c458e44
Minor dirty fix for final transcript dtypes.
stephaniesamm Jun 4, 2026
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 4 additions & 1 deletion .gitignore
Original file line number Diff line number Diff line change
@@ -1,2 +1,5 @@
data/
results/
results/

*__pycache__/
*.cache/
478 changes: 0 additions & 478 deletions code/clustering/Klimentova2022.tsv

This file was deleted.

Loading