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TheJacksonLaboratory
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diachromatic
Diachromatic is a Java application for preprocessing and quality control of Hi-C and CHi-C data.
https://diachromatic.readthedocs.io/en/latest/
GNU General Public License v3.0
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Add --keep-sam option to align command
#115
hansenp
closed
5 years ago
1
Error with name/path of temporary SAM file?
#114
pnrobinson
closed
5 years ago
6
Improve command-line error messages
#113
pnrobinson
closed
5 years ago
2
adding highcharts functionality to Truncator output
#112
pnrobinson
closed
5 years ago
3
Change items of text file output
#111
pnrobinson
closed
5 years ago
1
Adjust rst documentation for truncate
#110
pnrobinson
closed
5 years ago
2
test dataset
#109
pnrobinson
closed
5 years ago
2
highcharts
#108
pnrobinson
closed
5 years ago
1
FSI
#107
pnrobinson
closed
5 years ago
4
iBED
#106
pnrobinson
closed
5 years ago
2
Internal link
#105
pnrobinson
closed
5 years ago
3
Active
#104
pnrobinson
closed
5 years ago
3
RLC
#103
pnrobinson
closed
5 years ago
2
Create table with all quality metrics (RLC, CLC, etc.) for a decent number of datasets
#102
pnrobinson
closed
5 years ago
4
paired read pairs
#101
pnrobinson
closed
5 years ago
5
Dichromatic vs. HiCUP categories Table
#100
pnrobinson
closed
5 years ago
4
Graphic in map.rst
#99
pnrobinson
closed
5 years ago
1
Unligated pairs
#98
pnrobinson
closed
5 years ago
2
Size thresholds in mapping.rst
#97
pnrobinson
closed
5 years ago
3
Sizes of chimeric fragments
#96
pnrobinson
closed
5 years ago
2
Formation of Hi-C fragments
#95
pnrobinson
closed
5 years ago
0
Short options should have only one letter
#94
pnrobinson
closed
5 years ago
5
–sticky-ends option for truncate command should default to true
#93
pnrobinson
closed
5 years ago
1
truncate.rst
#92
pnrobinson
closed
5 years ago
3
Finish read pair categorization
#91
hansenp
closed
5 years ago
0
Perform simple/twisted analysis for promoter capture Hi-C analysis
#90
hansenp
closed
5 years ago
0
Show simple/twisted statistics as box plots (CTCF depeletion datasets)
#89
pnrobinson
closed
5 years ago
1
Choose datasets for simple/twisted analysis
#88
pnrobinson
closed
5 years ago
2
SVG generation to display results in HTML page
#87
pnrobinson
closed
5 years ago
1
Improve de dup map
#86
hansenp
closed
5 years ago
0
HTML output file
#85
pnrobinson
closed
5 years ago
2
First commit for HTML output file
#84
pnrobinson
closed
5 years ago
2
Count
#83
hansenp
closed
5 years ago
0
Remove conditions from interaction counts map
#82
hansenp
closed
5 years ago
1
Hashcodes
#81
pnrobinson
closed
5 years ago
1
JCommander
#80
pnrobinson
closed
5 years ago
0
Develop into master merge
#79
pnrobinson
closed
5 years ago
0
Self ligation threshold
#78
hansenp
closed
5 years ago
0
Current digest map insufficient if overhanging digest ends were filled in
#77
hansenp
closed
9 months ago
4
Removal of extra input file with coordinates of selected digests
#76
hansenp
closed
5 years ago
1
The truncation step of the pipeline attempts to address this situation by deleting the sequence that is downstream of the enzyme recognition site.
#75
pnrobinson
closed
5 years ago
8
ReadPair -- accessing static member via instace reference
#74
pnrobinson
closed
5 years ago
7
refactoring digest map
#73
pnrobinson
closed
5 years ago
2
Improve digest map
#72
pnrobinson
closed
5 years ago
0
Clean up align
#71
hansenp
closed
5 years ago
1
Clean up all classes assciated to the 'align' subcommand
#70
hansenp
closed
5 years ago
1
Consider merging classes InteractionCountsMap and Count
#69
pnrobinson
closed
5 years ago
1
Dedupmap
#68
pnrobinson
closed
5 years ago
3
Iss64 count command
#67
hansenp
closed
5 years ago
0
Allelespec
#66
pnrobinson
closed
5 years ago
1
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