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cerebis
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sim3C
Read-pair simulation of 3C-based sequencing methodologies (HiC, Meta3C, DNase-HiC)
GNU General Public License v3.0
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How to use sim3C to generate hic simulation data of different lengths according to the restriction site?
#41
xujialupaoli
opened
1 week ago
0
What does readID represent in the output simulation data?
#40
xujialupaoli
opened
1 week ago
0
Bugs with WGS read strandedness and R1/R2 FASTQ output
#39
solveforj
opened
4 months ago
0
Protocols employing dual-enzyme digests are not supported
#38
cerebis
closed
5 months ago
0
Validation checks for TOML profiles
#37
cerebis
closed
5 months ago
0
Added missing dependency to requirements.txt
#36
cerebis
closed
5 months ago
0
Expand readme to discuss newest additions
#35
cerebis
closed
5 months ago
0
Python3
#34
cerebis
closed
5 months ago
0
Replicon names are required to be unique across the entire community.
#33
cerebis
closed
5 months ago
0
Merging major change to master, resolves issue #29
#32
cerebis
closed
5 months ago
0
WGS read-pairs are always from the same segment
#31
cerebis
opened
5 months ago
0
Community profile format is cumbersome
#30
cerebis
opened
5 months ago
1
Fragmented replicons do not incur CIS interactions at the proper rate
#29
cerebis
closed
5 months ago
0
Reduce docker image size
#28
cerebis
closed
5 months ago
1
Annotations for community definitions
#27
cerebis
opened
5 months ago
1
Bug / problem at end of chromosomes
#26
ivargr
opened
1 year ago
3
Unrealistic with normal insert size between HiC read pairs?
#25
ivargr
closed
5 months ago
1
Add support for specifyign a bridge adapter for more complete simulation of Dnase Hi-C.
#24
ShunOuchi
closed
5 months ago
2
Bump numpy from 1.14.6 to 1.22.0
#23
dependabot[bot]
closed
5 months ago
2
Simulation without restriction enzymes
#22
ValentinaBoP
closed
5 months ago
1
Does sim3C accept self-prepared community abundance profile in Hi-C mode?
#21
zengxiaofei
closed
2 years ago
2
Bump pyyaml from 5.3.1 to 5.4
#20
dependabot[bot]
closed
5 months ago
2
Allow users to prescriptively modulate the interaction rates for specific coordinate pairs.
#19
jazberna1
opened
3 years ago
4
References without cut-sites should still produce spurious read-pairs and not just excluded from simulation.
#18
Mustafa-Albekaa
opened
3 years ago
4
Art.py warning level log should be debug level.
#17
cerebis
closed
5 months ago
0
problem in Installing sim3C
#16
sinamajidian
closed
4 years ago
5
FastQ header should be revised
#15
cerebis
closed
5 months ago
0
A potential hole in the documentation.
#14
cerebis
closed
5 months ago
0
The header format
#13
hsinnan75
closed
4 years ago
2
Empty fasta files raise exception generating abundance
#12
cerebis
closed
4 years ago
0
remove anti-diagonal for linear chromosomes
#11
Lila14
closed
4 years ago
0
Time-series integration
#10
cerebis
opened
5 years ago
1
Assess alternatives to BioPython as file IO is a bottle-neck
#9
cerebis
closed
5 months ago
1
Basic support for IUPAC symbols
#8
cerebis
closed
5 years ago
1
Example workflow and protocol
#7
lewkrr
closed
5 months ago
0
wrong type passed
#6
zeeev
closed
6 years ago
4
Fasta sequences which contain IUPAC characters other than ACGT throw an exception in Art.py
#5
Tocci89
closed
6 years ago
7
Chromosome copies cannot form inter-chr products.
#2
cerebis
opened
7 years ago
0
Spatial arrangement mediated _trans_ interactions
#1
cerebis
opened
7 years ago
0