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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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interrupted run restart?
#114
davidaray
closed
7 months ago
28
operands could not be broadcast together with shapes (2,) (11891,)
#124
edinatale
closed
2 months ago
9
OSError: Unable to open file
#130
zmz1988
closed
1 year ago
8
Issue on the merge of all chromosome in the post processing part.
#109
Manuel-Derrien
closed
1 year ago
6
upgrade dependencies
#117
teresi
closed
1 year ago
5
Annotation revision
#41
sjteresi
closed
3 years ago
5
compare_expression
#128
jordana-olive
opened
1 year ago
4
chi_squared_density_comparison.py not running
#122
amvarani
closed
1 year ago
4
Add relevant area calculation functions and tests
#40
sjteresi
closed
3 years ago
4
Resolve duplicate base assignment of TEs.
#31
sjteresi
closed
3 years ago
4
overlap to/from disk
#9
teresi
closed
4 years ago
4
post-processing
#144
asdfjohnny1
closed
7 months ago
3
Question about detecting unknown subfamily/order
#139
HLHsieh
closed
7 months ago
3
unequal set of chromosomes between datasets
#133
SolayMane
closed
1 year ago
3
Refactor revision code to NOT use pandas to_hdf
#127
sjteresi
closed
1 year ago
3
compare_expression.py
#123
amvarani
opened
1 year ago
3
Add relevant area calculation functions and tests
#27
sjteresi
closed
3 years ago
3
add MergeData test for summation
#24
teresi
opened
4 years ago
3
Scott merge overlap initial edits
#21
sjteresi
closed
4 years ago
3
Error occurred ?any help for me
#140
zhangwenda0518
closed
7 months ago
2
Can it be applied to 1Mb windows, instead of gene annotations?
#138
lcanesin
closed
2 months ago
2
regex pattern do not match
#134
SolayMane
opened
1 year ago
2
upgrade h5py
#121
teresi
closed
1 year ago
2
multithreading and speed
#115
davidaray
closed
7 months ago
2
New installation not reading hg data
#110
davidaray
closed
1 year ago
2
Error when no. of TE annotation chromosomes != no. gene annotation chromosomes
#108
sjteresi
closed
1 year ago
2
WIP fix progress update for density
#82
teresi
closed
3 years ago
2
Sense and Anti-Sense Density Values
#63
sjteresi
closed
2 years ago
2
Use read and write method of GeneData to save in h5 format.
#33
sjteresi
closed
3 years ago
2
Update to use GenomeData object and add additional graphs
#30
sjteresi
closed
3 years ago
2
add normalization matrices
#22
teresi
closed
3 years ago
2
add stub for test_Overlap
#18
teresi
closed
4 years ago
2
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
Stack limit reached ?
#142
asdfjohnny1
closed
9 months ago
1
Add new classmethod to initialize DensityData
#135
sjteresi
closed
1 year ago
1
Add helper information so that user's can see what pseudomolecules and TE groups they have
#129
sjteresi
closed
1 year ago
1
Begin refactoring of DensityData, refactor MSU HPCC submission scripts
#126
sjteresi
closed
1 week ago
1
Pytables Pickle warning for gene data
#118
sjteresi
closed
1 year ago
1
D/matching chromosomes
#113
sjteresi
closed
1 year ago
1
Bump numpy from 1.20.2 to 1.21.0 in /requirements
#105
dependabot[bot]
closed
2 years ago
1
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
Unclear Error Message for "Old" Overlap Values.
#96
sjteresi
opened
2 years ago
1
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
Explain and differentiate process.py, preprocess.py, and density.py
#57
sjteresi
closed
3 years ago
1
move output files outside of the code
#51
teresi
closed
1 year ago
1
fleshout log calls
#49
teresi
closed
3 years ago
1
fleshout argument parser help fields
#47
teresi
closed
3 years ago
1
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