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cerebis
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qc3C
Reference-free quality assessment for Hi-C sequencing data
GNU Affero General Public License v3.0
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Error: module 'numpy' has no attribute 'asscalar'
#63
shelkmike
opened
1 year ago
2
Enzyme-free protocol
#62
gubrins
closed
1 year ago
0
Support for Arima High coverage Hi-C kit
#61
Norbittner
opened
2 years ago
7
Provide greater detail when BAM sort order is incorrect.
#60
cerebis
closed
2 years ago
0
Failure to catch missing header exception
#59
cerebis
closed
2 years ago
2
Parsing of BAM header when file is expected to be readname-sorted.
#58
agilly
closed
2 years ago
7
Add ">20kbp" to the long-range pair counting statistic
#57
cerebis
opened
3 years ago
0
Accommodating mismatches in ligation artefacts.
#56
cerebis
opened
3 years ago
0
Input/Output documentation additiion
#55
cerebis
closed
3 years ago
0
Increase the maximum separation computed for BAM mode.
#54
cerebis
opened
3 years ago
0
Extended main help to better explain modes
#53
cerebis
opened
3 years ago
0
Validate mapping minimum quality limit with other mapping tools.
#52
cerebis
opened
3 years ago
0
Handling of split R1/R2 bam files
#51
cerebis
opened
3 years ago
0
Duplicates, flags, tallying and MultiQC report
#50
cerebis
opened
3 years ago
0
Add example data and results and extend docs
#49
cerebis
opened
3 years ago
1
Rename jellyfish conda package
#48
cerebis
opened
3 years ago
0
Old Linux distribution import error "GLIBC_2.23' not found"
#47
cerebis
opened
3 years ago
4
Cut-site databases saved to filesystem are not backwards portable to older Python.
#46
cerebis
opened
3 years ago
1
samtools missing from qc3C docker container path
#45
koadman
closed
3 years ago
1
qc3c missing from path when run via singularity
#44
koadman
closed
3 years ago
1
qc3C conda failure on CentOS8
#43
koadman
opened
3 years ago
4
Validate performance when kmer mode is supplied unpaired read data.
#42
cerebis
opened
3 years ago
0
Better bootstrap merged to master
#41
cerebis
closed
3 years ago
0
Conda package import error and problems using Docker image
#40
cerebis
opened
3 years ago
0
kmer lib creation options will not take effect of lib already exists
#39
cerebis
closed
4 years ago
0
Mergine multidigest branch into master
#38
cerebis
closed
4 years ago
0
Using longest ligation product can overestimate observed fraction
#37
cerebis
opened
4 years ago
0
Check for input files as soon as possible
#36
cerebis
opened
4 years ago
0
Natural occurrence estimation and correction
#35
cerebis
closed
4 years ago
9
Add command line meta-options for well known commercial libraries
#34
cerebis
closed
4 years ago
1
Environments with PYTHONPATH set can mislead docker image.
#33
cerebis
opened
4 years ago
0
Handle restriction enzymes with ambiguous sites
#32
cerebis
closed
4 years ago
1
Counting FastA returns 0
#31
cerebis
closed
4 years ago
0
Add version and time stamps to JSON report
#30
cerebis
closed
5 years ago
0
Add pigz to docker images
#29
cerebis
closed
5 years ago
0
Denominator in long-range fraction
#28
cerebis
closed
4 years ago
1
Kmer analysis is slow due to Jellyfish SWIG overhead.
#27
cerebis
opened
5 years ago
0
Running singularity container without arguments produces esoteric error message
#26
cerebis
closed
4 years ago
1
Improve docker useability after more use
#25
cerebis
closed
4 years ago
1
qc3C depends on samtools
#24
cerebis
closed
5 years ago
1
qc3C docker and singularity
#23
cerebis
closed
5 years ago
1
Reports from kmer and bam modes should as consistent as possible.
#22
cerebis
closed
5 years ago
0
Add docker/singlularity details to documentation
#21
cerebis
closed
5 years ago
0
could track both full cut-site and vestigal
#20
cerebis
closed
4 years ago
1
Validate on less commonly used enzymes
#19
cerebis
closed
4 years ago
2
Fuzzier evidence of junctions
#18
cerebis
closed
5 years ago
0
In bam mode, report fraction against long references
#17
cerebis
closed
5 years ago
0
Output report in easily parsed format
#16
cerebis
closed
5 years ago
1
Improve comment about fraction of reads starting with site
#15
cerebis
closed
5 years ago
0
update read me for new CLI changes
#14
cerebis
closed
5 years ago
0
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