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
Add check for non-unique genes, which causes overlap broadcast error
#147
sjteresi
closed
2 months ago
0
How to interpret the outcome document? Help me
#146
zhangwenda0518
opened
5 months ago
1
Plotting the results in R
#145
hoyosmanuel
closed
2 months ago
1
post-processing
#144
asdfjohnny1
closed
7 months ago
3
add error message for revision
#143
teresi
closed
7 months ago
0
Stack limit reached ?
#142
asdfjohnny1
closed
9 months ago
1
fleshout exception message on import_filtered_genes
#141
teresi
closed
7 months ago
0
Error occurred ？any help for me
#140
zhangwenda0518
closed
7 months ago
2
Question about detecting unknown subfamily/order
#139
HLHsieh
closed
7 months ago
3
Can it be applied to 1Mb windows, instead of gene annotations?
#138
lcanesin
closed
2 months ago
2
initial merge data / density data refactor
#137
teresi
closed
11 months ago
0
add setup.py
#136
teresi
closed
1 year ago
0
Add new classmethod to initialize DensityData
#135
sjteresi
closed
1 year ago
1
regex pattern do not match
#134
SolayMane
opened
1 year ago
2
unequal set of chromosomes between datasets
#133
SolayMane
closed
1 year ago
3
F/refactor gene te data h5
#132
sjteresi
closed
1 year ago
0
refactor
#131
teresi
closed
1 year ago
0
OSError: Unable to open file
#130
zmz1988
closed
1 year ago
8
Add helper information so that user's can see what pseudomolecules and TE groups they have
#129
sjteresi
closed
1 year ago
1
compare_expression
#128
jordana-olive
opened
1 year ago
4
Refactor revision code to NOT use pandas to_hdf
#127
sjteresi
closed
1 year ago
3
Begin refactoring of DensityData, refactor MSU HPCC submission scripts
#126
sjteresi
closed
3 hours ago
1
upgrade dependencies
#125
teresi
closed
1 year ago
0
operands could not be broadcast together with shapes (2,) (11891,)
#124
edinatale
closed
2 months ago
9
compare_expression.py
#123
amvarani
opened
1 year ago
3
chi_squared_density_comparison.py not running
#122
amvarani
closed
1 year ago
4
upgrade h5py
#121
teresi
closed
1 year ago
2
WIP f/chunk
#120
teresi
closed
1 year ago
0
Fix method to correctly address edge case of missing data.
#119
sjteresi
closed
1 year ago
0
Pytables Pickle warning for gene data
#118
sjteresi
closed
1 year ago
1
upgrade dependencies
#117
teresi
closed
1 year ago
5
F/manager context
#116
teresi
closed
1 year ago
0
multithreading and speed
#115
davidaray
closed
7 months ago
2
interrupted run restart?
#114
davidaray
closed
7 months ago
28
D/matching chromosomes
#113
sjteresi
closed
1 year ago
1
D/additional user help density data
#112
sjteresi
closed
1 year ago
0
Add check to make sure valid GFF strand values exist
#111
sjteresi
closed
1 year ago
0
New installation not reading hg data
#110
davidaray
closed
1 year ago
2
Issue on the merge of all chromosome in the post processing part.
#109
Manuel-Derrien
closed
1 year ago
6
Error when no. of TE annotation chromosomes != no. gene annotation chromosomes
#108
sjteresi
closed
1 year ago
2
Refactor post-processing of output to be unnecessary, perform during normal pipeline.
#107
sjteresi
closed
3 hours ago
0
Add more documentation and helpful user scripts
#106
sjteresi
closed
2 years ago
0
Bump numpy from 1.20.2 to 1.21.0 in /requirements
#105
dependabot[bot]
closed
2 years ago
1
F/reviewer comments
#104
sjteresi
closed
2 years ago
0
F/reviewer comments
#103
sjteresi
closed
2 years ago
0
Bump pillow from 8.2.0 to 8.3.2 in /requirements
#102
dependabot[bot]
closed
2 years ago
1
Bump py from 1.8.0 to 1.10.0 in /requirements
#101
dependabot[bot]
closed
2 years ago
1
Code cleanup and general documentation prior to publication
#100
sjteresi
closed
2 years ago
0
Refactor MergeData manager out of process_genome.py
#99
sjteresi
opened
2 years ago
0
F/go enrichment
#98
sjteresi
closed
2 years ago
0
Next