GEP2 v0.2.1 beta

Patch version. Several bugs were fixed.

GEP2 v0.2.0 beta

IMPORTANT: delete the previous GEP2_env conda envirnment and create a new one!

Added Hi-C Analysis (chromap, pretext, cooler, tracks for curation!)
Added Inspector Analysis
Local mode tested
Improved temp dir logic

To-Do:

Code cleaning with AI tools
Fix convert md to pdf
NomNom now on conda forge
Simplified GEP2 conda env
BUSCO option (default still is Compleasm)
FASTK option (default still is Meryl)
Blob-plot for contamination
FCS-GX
Chrom Plots
EAR integration
GEP2 super report

GEP2 v0.1.1-alpha

Patch for 10x dataset.
Patch for NomNom.
Improved downloads validatio.
New temp dir logic.
New column in data table for better flexibility.

To-Do:

Code cleaning with AI tools
Test in local mode
Fix convert md to pdf
Inspector Analysis
Hi-C Pretext maps & stats
Pretext tracks for curation
NomNom now on conda forge
Simplified GEP2 conda env
BUSCO option (default still is Compleasm)
FASTK option (default still is Meryl)
Blob-plot for contamination
FCS-GX
Chrom Plots
EAR integration
GEP2 super report

v0.1.0-alpha

GEP2 v0.1.0-alpha

Initial release of GEP2

To-Do:

• Code cleaning with AI tools
• Test in local mode
• Test 10x datasets
• Fix convert md to pdf
• Inspector Analysis
• Hi-C Pretext maps & stats
• Pretext tracks for curation
• NomNom now on conda forge
• Simplified GEP2 conda env
• BUSCO option (default still is Compleasm)
• FASTK option (default still is Meryl)
• Blob-plot for contamination
• FCS-GX
• Chrom Plots
• EAR integration
• GEP2 super report