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dputhier
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pygtftk
A python package and a set of shell commands to handle GTF files
GNU General Public License v3.0
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[ologram] -- Features whose size is always 1 should not be tested.
#85
dputhier
closed
5 years ago
2
Example with lots of warnings in 1.0.5
#84
dputhier
closed
5 years ago
0
User-friendly adjustements to exposed arguments
#83
guillaumecharbonnier
closed
5 years ago
4
Replace minibatch-nb and minibatch-size with max-ram
#82
guillaumecharbonnier
closed
5 years ago
1
Bad nb-threads default
#81
guillaumecharbonnier
closed
5 years ago
7
Implement strategy for N-fold bed samples comparison
#80
guillaumecharbonnier
closed
3 years ago
5
Implement strategy when key has more than 50 values
#79
guillaumecharbonnier
closed
5 years ago
13
Relaxing constraints on GTF format
#78
guillaumecharbonnier
closed
5 years ago
4
Warnings
#77
qferre
closed
5 years ago
2
[ologram] -- issue with chromosomes in ensembl format
#76
dputhier
closed
5 years ago
1
[ologram]: FutureWarnings ...
#75
yaskermezli
closed
5 years ago
5
provide user with default exclude regions.
#74
dputhier
closed
5 years ago
2
add an --include-region argument
#73
dputhier
closed
5 years ago
2
[ologram] P-values equal to zero when nb_intersections_true and nb_intersections_esperance_shuffled are equal to zero.
#72
dputhier
closed
5 years ago
6
#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION
#71
dputhier
closed
5 years ago
1
ologram: libgcc_s.so.1 must be installed for pthread_cancel to work
#70
dputhier
closed
5 years ago
1
Unable to build conda package under OSX
#69
dputhier
closed
5 years ago
0
[ologram] Re-use mini_real in documentation
#68
qferre
closed
5 years ago
4
[ologram] Cython multiprocessing error
#67
qferre
closed
5 years ago
15
[peak_anno] Undefined chromosome error
#66
Norisad
closed
5 years ago
15
[peak_anno] Name change
#65
qferre
closed
5 years ago
10
peak_anno: GTF should be facultative
#64
dputhier
closed
5 years ago
1
[peak_anno] Optional pdf
#63
qferre
closed
5 years ago
1
peak_anno -K
#62
dputhier
closed
5 years ago
1
[peak_anno] Negative Binomial Fitting
#61
qferre
closed
5 years ago
1
test peak_anno_2 and peak_anno_4 are failing (at least under OSX).
#60
dputhier
closed
5 years ago
2
peak_anno: negbin_fit.py:86: RuntimeWarning: invalid value encountered in double_scalars return np.sqrt(chi2 / (n*(min(crosstab.shape)-1)))
#59
dputhier
closed
5 years ago
4
peak_anno: RuntimeWarning: divide by zero encountered in log return log(self._cdf(x, *args))
#58
dputhier
closed
5 years ago
4
peak_anno complains about hg38.genome no existing but too late
#57
dputhier
closed
5 years ago
2
Tests not passing in conda build git develop
#56
guillaumecharbonnier
closed
5 years ago
15
[ologram] almost all p-values set to p=1.11e-16
#55
dputhier
closed
5 years ago
5
peak_anno : several errors encountered in example file (rst)
#54
dputhier
closed
5 years ago
15
from __future__ should be discarded
#53
dputhier
closed
5 years ago
1
Peak anno shuffling
#52
qferre
closed
5 years ago
3
peak_anno: "frequencies has a zero element at %s." % (zeropos,)) ValueError: The internally computed table of expected frequencies has a zero element at (13, 0).
#51
dputhier
closed
5 years ago
8
peakanno and default chrom size
#50
dputhier
closed
5 years ago
7
Exit code 247 on readthedoc
#49
dputhier
closed
5 years ago
0
Create CODE_OF_CONDUCT.md
#48
dputhier
closed
5 years ago
0
Segfault when using bed3 files
#47
qferre
closed
5 years ago
24
Code improvement
#46
dputhier
closed
5 years ago
1
retrieve usage in interpreter
#45
dputhier
closed
5 years ago
1
check self.__dict__ upon deletion of an attribute
#44
dputhier
closed
5 years ago
0
hide_undef is not supported by extract_data when a TAB object is returned
#43
dputhier
closed
5 years ago
1
peak_anno error upon installation
#42
dputhier
closed
5 years ago
2
argformatter: bed6 and FileWithExtension should be merge
#41
dputhier
closed
5 years ago
1
gtftk retrieve -c and -o should be mutually exclusive
#40
dputhier
closed
5 years ago
1
argparse should not be a dependency
#39
dputhier
closed
5 years ago
2
gtftk main program complains when an unknow argument is passed
#38
dputhier
closed
5 years ago
1
For test reproducibility chrom_info_as_dict should use an OrderedDict instead of a defaultDict
#37
dputhier
closed
5 years ago
1
ArgFormatter.bed6
#36
qferre
closed
5 years ago
1
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