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deeptools
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HiCExplorer
HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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How to make the PC1 value more comparable accross chromosomes and samples
#709
biozzq
closed
3 years ago
2
using corrected cool file instead of h5 file in the subcommand of hicexplorer
#708
biozzq
closed
3 years ago
1
hicMergeMatrixBins on an uncorrected matrix built at specific resolution
#707
biozzq
closed
3 years ago
8
hicCorrectMatrix sometimes crashes with cool format
#706
cgirardot
closed
3 years ago
3
Control of hicPlotTads output image width?
#705
ArielPaulson
closed
3 years ago
2
How to remove inter-chromosomal interactions from matrix
#704
cgirardot
closed
3 years ago
4
error in file order
#703
jiangshan529
closed
3 years ago
16
Version 2.2.1.1 working fine, except for hicDifferentialTAD and hicDetectLoops
#702
ArielPaulson
closed
3 years ago
8
hicFindRestSite galaxy wrapper 3.6 complains about restriction enzyme sequence
#701
cgirardot
closed
3 years ago
8
Issue merging reads
#700
StefanoLonardi
closed
3 years ago
3
scaling P(s) request
#699
kimj50
closed
3 years ago
1
hicAggregateContacts error
#698
robeach78
closed
3 years ago
3
Parameter combination issues about hicCorrectMatrix
#697
biozzq
closed
3 years ago
2
Plot dist vs counts
#696
lldelisle
closed
3 years ago
1
numpy error
#695
e-lerat
closed
3 years ago
4
chicViewpoint --writeFileNamesToFile
#694
Jssmith91
closed
3 years ago
6
Albert tad
#693
AlbertLidel
closed
3 years ago
0
Albert tad
#692
AlbertLidel
closed
3 years ago
1
new biopython version incompatible with HiCExplorer
#691
bgruening
closed
3 years ago
7
hicConvertFormat hic to h5 exits silently without output
#690
mdozmorov
closed
3 years ago
2
Dev hic tad classifier
#689
AlbertLidel
closed
3 years ago
0
HiCExplorer with Micro-C data
#688
StephenRicher
closed
3 years ago
5
hicPlotMatrix from .hic file issue
#687
ptranvan
closed
3 years ago
1
variation in Boundary size after matrix correction
#686
mujahida87
closed
3 years ago
4
ERROR:hicexplorer.hicDifferentialTAD:local variable 'right_boundary_index_target' referenced before assignmentTraceback
#685
antarikshtyagi
closed
3 years ago
7
Is there a recogmended protein profile for loops ?
#684
gnilihzeux
closed
3 years ago
2
sample downsizing of Hi-C data to equalize data set of variable sequencing depth
#683
mujahida87
closed
3 years ago
2
hicPlotTADs does not produce hic matrix in the plot
#682
antarikshtyagi
closed
3 years ago
8
Clarifications of parameters
#681
gdolsten
closed
3 years ago
11
Varying bin size in *_tad_score.bm
#680
yancychy
closed
3 years ago
1
Boundary size difference after matrix correction
#679
Drosophilid
closed
3 years ago
15
hicplotTADs show same range for ICE and KR normalization
#678
yancychy
closed
3 years ago
1
hicCompareMatrices without normalization
#677
yxsee
closed
3 years ago
1
Zero loops?
#676
gdolsten
closed
3 years ago
2
hicFindRestSite ImportError: Bio.Alphabet has been removed from Biopython.
#675
LuminescentBeing
closed
3 years ago
9
downsample Hi-C contacts/equalisation of valid pairs between different samples
#674
Drosophilid
closed
3 years ago
1
hicBuildMatrix complains about read order
#673
cgirardot
closed
3 years ago
15
hicPCA run of memory for 10kb resolution for Drosaphila
#672
yancychy
closed
3 years ago
4
hicNormalize is really slow
#671
cgirardot
closed
3 years ago
7
Runtime questions
#670
gdolsten
closed
3 years ago
3
Option to generate just one eigenvector and, separately, select which one you want
#669
kalavattam
closed
3 years ago
0
HiC Matrix visualization
#668
gdolsten
closed
3 years ago
1
Difficulties installing HiCExplorer using conda
#667
gdolsten
closed
3 years ago
3
HiCExplorer crashes on small dataset
#666
nservant
closed
3 years ago
16
hicBuildMatrix ends with KeyError
#665
cgirardot
closed
3 years ago
4
Plot whole genome excluding intra-chromosomal (cis) contacts (i.e., show only trans contacts)?
#664
kalavattam
closed
3 years ago
2
Adapter trimming of fastq Hi-C raw reads
#663
Drosophilid
closed
3 years ago
3
Error:'Some.cool' is not an HDF5 file when using hicPlotMatrix
#662
jiangshan529
closed
3 years ago
48
Clarification on application of Juicer KR correction factors to HiCExplorer hic2cool-converted matrices
#661
kalavattam
closed
3 years ago
9
chromatin state border color issue
#660
Drosophilid
closed
3 years ago
8
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