issues
search
sjteresi
/
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
28
stars
4
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
How to interpret the process density progress bar
#97
sjteresi
opened
2 years ago
0
Unclear Error Message for "Old" Overlap Values.
#96
sjteresi
opened
2 years ago
1
Refactor usage of term "Intronic" to "Intragenic"
#95
sjteresi
closed
2 years ago
0
F/arabidopsis dotplot
#94
sjteresi
closed
2 years ago
0
F/human exhibition
#93
sjteresi
closed
2 years ago
0
F/human exhibition
#92
sjteresi
closed
2 years ago
0
Add code to re-create Blueberry gene expression analysis example
#91
sjteresi
closed
2 years ago
0
F/rice synteny
#90
sjteresi
closed
2 years ago
0
Bug/import anno float
#89
sjteresi
closed
3 years ago
0
Working sbatch code
#88
sjteresi
closed
3 years ago
0
Fix creation of needed directories
#87
sjteresi
closed
2 years ago
0
revise annotation test failures
#86
teresi
closed
2 years ago
0
minor refactoring in sum
#85
teresi
closed
3 years ago
0
fix progress bar
#84
teresi
closed
3 years ago
0
add profiling & fix major bottleneck
#83
teresi
closed
3 years ago
0
WIP fix progress update for density
#82
teresi
closed
3 years ago
2
fix missing density output
#81
teresi
closed
3 years ago
0
add superfamily / order names to density output
#80
teresi
closed
3 years ago
0
fix gene counter
#79
teresi
closed
3 years ago
0
F/multi density
#78
teresi
closed
3 years ago
0
fix intra density calcs
#77
teresi
closed
3 years ago
0
Fix revision tests
#76
sjteresi
closed
3 years ago
0
Working order revision tests and fixture parametrization
#75
sjteresi
closed
3 years ago
0
first working density calcs
#74
teresi
closed
3 years ago
0
initial commit post meeting with Mike
#73
teresi
closed
3 years ago
0
fix bad tests
#72
sjteresi
closed
3 years ago
0
F/overlap files cache
#71
teresi
closed
3 years ago
0
B/functools cache
#70
teresi
closed
3 years ago
0
refactor overlap output location
#69
teresi
closed
3 years ago
0
Begin fixes for slicing and use of normalization methods
#68
sjteresi
closed
3 years ago
0
Norm in mergedata
#67
sjteresi
closed
3 years ago
0
Refactor overlap
#66
teresi
closed
3 years ago
0
Graph Density Results Over Each Window by TE Type
#65
sjteresi
closed
3 years ago
1
Generate TPM and FPKM Matrix for Strawberry Fruit Expression Dataset
#64
sjteresi
closed
3 years ago
1
Sense and Anti-Sense Density Values
#63
sjteresi
closed
2 years ago
2
Update README
#62
sjteresi
closed
2 years ago
0
Refactor genome_id usage to be inherent to the dataframe
#61
sjteresi
closed
3 years ago
0
F/make gene data transposon data
#60
teresi
closed
3 years ago
0
add ctags
#59
teresi
closed
3 years ago
0
Add yield statements and h5 cache creation
#58
sjteresi
closed
3 years ago
0
Explain and differentiate process.py, preprocess.py, and density.py
#57
sjteresi
closed
3 years ago
1
add more preprocessing refactor
#56
teresi
closed
3 years ago
0
Mergedata test new
#55
teresi
closed
3 years ago
0
Update log calls
#54
sjteresi
closed
3 years ago
0
Update file paths. process.py executes correctly
#53
sjteresi
closed
3 years ago
0
begin preprocess refactor
#52
teresi
closed
3 years ago
0
move output files outside of the code
#51
teresi
closed
1 year ago
1
add one liner docstrings
#50
teresi
closed
2 years ago
0
fleshout log calls
#49
teresi
closed
3 years ago
1
consolidate preprocessing
#48
teresi
closed
2 years ago
0
Previous
Next