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logsdon-lab
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CenMAP
Centromere mapping and annotation pipeline
MIT License
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feat: CI Dockerhub upload
#80
koisland
closed
1 day ago
0
Trimming doesn't remove gaps at edges
#79
koisland
opened
1 day ago
0
feat: CDR-Finder
#78
koisland
closed
1 day ago
0
bugfix: Better mapping and usage
#77
koisland
closed
3 days ago
0
bugfix: Change submodule url.
#76
koisland
closed
1 week ago
0
Add orientation of AS-HOR monomer to complete plot
#75
koisland
opened
2 weeks ago
0
CenMap running stopped at installing pip dependencies step (ModDotPlot)
#74
chunlinxiao
opened
2 weeks ago
18
bugfix: ModDotPlot version
#73
koisland
closed
2 weeks ago
0
CHM13 repeatmasker and HOR stv annotation coordinates differ
#72
koisland
opened
1 month ago
0
bugfix: Fix checking deployment method and empty HOR length file
#71
koisland
closed
1 month ago
0
feat: Docker and plot fixes
#70
koisland
closed
1 month ago
0
Switch from GitHub modules to gitmodules
#69
koisland
opened
1 month ago
0
Create Dockerfile
#68
koisland
closed
1 month ago
0
bugfix: Multiple HOR lengths for reference
#67
koisland
closed
1 month ago
0
feat: Refactor AS-HOR filter
#66
koisland
closed
1 month ago
0
feat: Download CHM13 Reference
#65
koisland
closed
1 month ago
0
feat: Snakemake v8
#64
koisland
closed
1 month ago
0
feat: RepeatMasker before NucFlag
#63
koisland
closed
1 month ago
0
Add step to download CHM13 reference genome
#62
koisland
closed
1 month ago
0
feat: Cleanup and `nucflag` workflow changes
#61
koisland
closed
1 month ago
0
Move `map_cens.py` and `filter_dnabrnn_output.py` scripts to `CenStats`
#60
koisland
opened
1 month ago
0
Make more intermediate files temporary.
#59
koisland
closed
1 month ago
0
Allow passing `.fofn` for NucFlag
#58
koisland
closed
1 month ago
0
Add annotations to single plot
#57
koisland
closed
1 month ago
0
bugfix: Correct RM coordinates in contig name
#56
koisland
closed
2 months ago
0
bugfix/feat: Improved mapping, trimming, and ease-of-use
#55
koisland
closed
2 months ago
0
rename_ctgs rule fails on assembly fasta names without colon.
#54
koisland
closed
2 months ago
0
Add ability to omit step via configfile.
#53
koisland
closed
2 months ago
0
Replace bedminmax script with bedtools groupby
#52
koisland
closed
1 month ago
0
feat: Refactor Cen Counts
#51
koisland
closed
4 months ago
0
bugfix: Missing chr16 Centromeres
#50
koisland
closed
4 months ago
0
Change bedminmax steps to conserve pq arm information.
#49
koisland
closed
2 months ago
0
chr16 Filtering Issue
#48
koisland
closed
4 months ago
0
Move counting number of cens to after HOR array length calculation
#47
koisland
closed
4 months ago
0
Round complete centromere proportions to 1 decimal place
#46
koisland
closed
4 months ago
0
Remove rename_ctgs module and replace with seqkit replace
#45
koisland
closed
1 month ago
0
feat: ModDotPlot and Cen Improvements
#44
koisland
closed
4 months ago
0
Move ModDotPlot histogram to bottom right
#43
koisland
closed
4 months ago
0
hotfix: Remove empty fasta check and fix colors
#42
koisland
closed
4 months ago
0
Repeat Annotation Colorscale is Muted
#41
koisland
closed
4 months ago
0
No cens for a specific chr causes unnecessary crash
#40
koisland
closed
4 months ago
0
feat: Full CI Run
#39
koisland
closed
4 months ago
0
bugfix: ModDotPlot Cen Plotting Workflow Fixes
#38
koisland
closed
4 months ago
0
feat: HOR Array Length Refactor
#37
koisland
closed
4 months ago
0
feat: Replace StainedGlass with ModDotPlot
#36
koisland
closed
4 months ago
0
hotfix: Incorrect assembly for NucFlag
#35
koisland
closed
4 months ago
0
feat: NucFlag and RepeatMasker Refactor
#34
koisland
closed
4 months ago
0
Incorrect chr1 HOR monomer Classification
#33
koisland
opened
4 months ago
0
doc: Use GH Wiki and Cleanup
#32
koisland
closed
4 months ago
0
bugfix: Mismapping Fixes
#31
koisland
closed
4 months ago
0
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