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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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Error "Unable to open object (object 'RHO_SUPERFAMILIES_RIGHT' doesn't exist)
#156
PraveenOraon
opened
2 weeks ago
1
Update text and column names for Intragenic values, when parsed with Density Utils
#155
sjteresi
closed
1 month ago
0
Are .h5 files empty?
#154
LeoVincenzi
closed
1 week ago
4
general_read_density_data.py
#153
dwx741886
closed
4 months ago
12
Refactor example output data reading script
#152
sjteresi
closed
5 months ago
0
Add presentation from CSHL 2022
#151
sjteresi
opened
5 months ago
0
genome-wide plots
#150
FlaviaTG
closed
5 months ago
3
OSError during process density
#149
FlaviaTG
closed
5 months ago
2
Output data analysis: Make table generation more robust for people with fragmented data
#148
sjteresi
closed
2 months ago
0
Add check for non-unique genes, which causes overlap broadcast error
#147
sjteresi
closed
9 months ago
0
How to interpret the outcome document? Help me
#146
zhangwenda0518
opened
12 months ago
1
Plotting the results in R
#145
hoyosmanuel
closed
9 months ago
1
post-processing
#144
asdfjohnny1
closed
1 year ago
3
add error message for revision
#143
teresi
closed
1 year ago
0
Stack limit reached ?
#142
asdfjohnny1
closed
1 year ago
1
fleshout exception message on import_filtered_genes
#141
teresi
closed
1 year ago
0
Error occurred ？any help for me
#140
zhangwenda0518
closed
1 year ago
2
Question about detecting unknown subfamily/order
#139
HLHsieh
closed
1 year ago
3
Can it be applied to 1Mb windows, instead of gene annotations?
#138
lcanesin
closed
9 months ago
2
initial merge data / density data refactor
#137
teresi
closed
1 year 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
closed
5 months 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
6 months ago
1
upgrade dependencies
#125
teresi
closed
1 year ago
0
operands could not be broadcast together with shapes (2,) (11891,)
#124
edinatale
closed
9 months ago
9
compare_expression.py
#123
amvarani
closed
6 months ago
3
chi_squared_density_comparison.py not running
#122
amvarani
closed
2 years ago
4
upgrade h5py
#121
teresi
closed
2 years ago
2
WIP f/chunk
#120
teresi
closed
2 years ago
0
Fix method to correctly address edge case of missing data.
#119
sjteresi
closed
2 years ago
0
Pytables Pickle warning for gene data
#118
sjteresi
closed
2 years ago
1
upgrade dependencies
#117
teresi
closed
2 years ago
5
F/manager context
#116
teresi
closed
2 years ago
0
multithreading and speed
#115
davidaray
closed
1 year ago
2
interrupted run restart?
#114
davidaray
closed
1 year ago
28
D/matching chromosomes
#113
sjteresi
closed
2 years ago
1
D/additional user help density data
#112
sjteresi
closed
2 years ago
0
Add check to make sure valid GFF strand values exist
#111
sjteresi
closed
2 years ago
0
New installation not reading hg data
#110
davidaray
closed
2 years ago
2
Issue on the merge of all chromosome in the post processing part.
#109
Manuel-Derrien
closed
2 years ago
6
Error when no. of TE annotation chromosomes != no. gene annotation chromosomes
#108
sjteresi
closed
2 years ago
2
Refactor post-processing of output to be unnecessary, perform during normal pipeline.
#107
sjteresi
closed
6 months ago
0
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