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encode of isoform and gene names is problematic

cleanupCode cleanup and simplificationCode cleanup and simplification

Status: Open.

#549 In BrooksLabUCSC/flair;

· diekhans opened on Jul 9, 2025

 ·  

FLAIR 3.0

use sphinx autodoc to generate command line in documentation

Status: Open.

#547 In BrooksLabUCSC/flair;

· diekhans opened on Jul 9, 2025

 ·  

FLAIR 3.0

rewrite runDS and runDE in R

cleanupCode cleanup and simplificationCode cleanup and simplification

mod; diffexp

mod; diffsplice

Status: Open.

#545 In BrooksLabUCSC/flair;

· diekhans opened on Jul 8, 2025

Add acknowlegments to packages that are used by FLAIR to documentation

Status: Open.

#542 In BrooksLabUCSC/flair;

· diekhans opened on Jul 4, 2025

 ·  

FLAIR 3.0

replace use of ncls package

Status: Open.

#541 In BrooksLabUCSC/flair;

· diekhans opened on Jul 4, 2025

Create working example for users.

DocumentationUpdate ReadTheDocs manualUpdate ReadTheDocs manual

Status: Open.

#540 In BrooksLabUCSC/flair;

· diekhans opened on Jul 3, 2025

Have flair-dev always include diffexp dependencies and run tests

Status: Open.

#538 In BrooksLabUCSC/flair;

· diekhans opened on Jul 3, 2025

 ·  

FLAIR 3.0

FLAIR align read prefiltering improvements

Status: Open.

#527 In BrooksLabUCSC/flair;

· cafelton opened on Jul 1, 2025

 ·  

FLAIR 3.1

Flair quantify stuck

Status: Open.

#524 In BrooksLabUCSC/flair;

· Olabanjiphil1 opened on Jun 27, 2025

Add bedPartition to FLAIR for FLAIR 3 release

Status: Open.

#519 In BrooksLabUCSC/flair;

· cafelton opened on Jun 25, 2025

 ·  

FLAIR 3.0

FLAIR 3.1 release planning

Status: Open.

#518 In BrooksLabUCSC/flair;

· cafelton opened on Jun 25, 2025

 ·  

FLAIR 3.1

Understand, document, and cenrtalize all name parsing and assumtions

Status: Open.

#516 In BrooksLabUCSC/flair;

· diekhans opened on Jun 19, 2025