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sjteresi
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TE_Density
Python script calculating transposable element density for all genes in a genome. Publication: https://mobilednajournal.biomedcentral.com/articles/10.1186/s13100-022-00264-4
GNU General Public License v3.0
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fleshout log calls
#49
teresi
closed
3 years ago
1
consolidate preprocessing
#48
teresi
closed
2 years ago
0
fleshout argument parser help fields
#47
teresi
closed
3 years ago
1
add sundry fixes for status updates / formatting
#46
teresi
closed
3 years ago
0
Refactor density to process and preprocess
#45
sjteresi
closed
3 years ago
1
delete inactive branches
#44
teresi
closed
8 months ago
0
format
#43
teresi
closed
3 years ago
1
add documentation
#42
teresi
closed
2 years ago
0
Annotation revision
#41
sjteresi
closed
3 years ago
5
Add relevant area calculation functions and tests
#40
sjteresi
closed
3 years ago
4
Save a sorted dataframe to disk
#39
sjteresi
closed
3 years ago
0
Update default string for H5 cache
#38
sjteresi
closed
3 years ago
0
Update H5 cache read and write methods
#37
sjteresi
closed
3 years ago
0
Annotation revision
#36
sjteresi
closed
3 years ago
0
add initial worker / manager for overlaps
#35
teresi
closed
3 years ago
0
Update requirements.txt
#34
sjteresi
closed
3 years ago
0
Use read and write method of GeneData to save in h5 format.
#33
sjteresi
closed
3 years ago
2
add merge manager / worker
#32
teresi
closed
3 years ago
1
Resolve duplicate base assignment of TEs.
#31
sjteresi
closed
3 years ago
4
Update to use GenomeData object and add additional graphs
#30
sjteresi
closed
3 years ago
2
Standardize EDTA Naming Scheme
#29
sjteresi
closed
3 years ago
1
bugfix OverlapData overuse of RAM when opening existing file
#28
teresi
closed
4 years ago
0
Add relevant area calculation functions and tests
#27
sjteresi
closed
4 years ago
3
sum overlap values
#26
teresi
closed
4 years ago
0
add normalization
#25
teresi
closed
2 years ago
0
add MergeData test for summation
#24
teresi
opened
4 years ago
3
add merge worker
#23
teresi
closed
1 year ago
0
add normalization matrices
#22
teresi
closed
3 years ago
2
Scott merge overlap initial edits
#21
sjteresi
closed
4 years ago
3
merge overlap (initial)
#20
teresi
closed
4 years ago
1
Multipie graph creation
#19
sjteresi
closed
4 years ago
1
add stub for test_Overlap
#18
teresi
closed
4 years ago
2
Fix edge case math, for window length
#17
sjteresi
closed
4 years ago
0
add windows read/write to overlap file
#16
teresi
closed
4 years ago
0
Import cache
#15
sjteresi
closed
4 years ago
0
Functionality to customize overlap data output location
#14
sjteresi
closed
4 years ago
1
refactor data.py by moving each class to its own file
#13
teresi
closed
4 years ago
0
Update config file usage, add new optional argument to density
#12
sjteresi
closed
4 years ago
1
add unique chromosome identifier to GeneData
#11
teresi
closed
4 years ago
0
write/read gene names to overlap file
#10
teresi
closed
4 years ago
1
overlap to/from disk
#9
teresi
closed
4 years ago
4
H5py
#8
sjteresi
closed
4 years ago
0
Early h5py methods
#7
sjteresi
closed
4 years ago
0
add Overlap, OverlapData for calculating TE / gene overlaps
#6
teresi
closed
4 years ago
1
Feature/cleanup preprocessing
#5
teresi
closed
4 years ago
0
- fix test & function for `rho_left_window`
#4
teresi
closed
4 years ago
0
- use if / raise not try / assert / catch / raise
#3
teresi
closed
4 years ago
0
Feature/refactor rho tests
#2
teresi
closed
4 years ago
0
Origin/feature/density
#1
sjteresi
closed
4 years ago
0
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