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gamcil
/
clinker
Gene cluster comparison figure generator
MIT License
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Feature Request: show gene label only for genes creating clusters
#61
pdec
opened
3 years ago
0
Running Clinker on a Server?
#60
Robaina
closed
2 years ago
3
Error when using gff file as input
#59
TsumaR
opened
3 years ago
0
Add scaffold ranges
#58
gamcil
closed
3 years ago
0
Feature Request: Incomplete/disrupted genes in the figure
#57
janpal-cz
opened
3 years ago
1
Add scaffold ranges
#56
gamcil
closed
3 years ago
0
extend sub matrix alphabets to avoid exceptions during alignment
#55
gamcil
closed
3 years ago
0
fix mock div element when saving svg
#54
gamcil
closed
3 years ago
0
Colour additions
#53
gamcil
closed
3 years ago
0
Group restoration when inst. Globaligner from dict
#52
lukas-val
closed
3 years ago
1
Groups are not restored during session loading
#51
lukas-val
closed
3 years ago
2
Replace consolidation with a disjoint-set data structure
#50
althonos
closed
3 years ago
1
RecursionError in `clinker.align.consolidate` (and a proposed fix)
#49
althonos
closed
3 years ago
2
Maximum recursion depth exceeded
#48
chanana
closed
3 years ago
3
Groups refactor
#47
gamcil
closed
3 years ago
0
Changing color of a gene to a specific desired color
#46
Cereben
closed
3 years ago
4
"This SVG is not valid, validate it before opening"
#45
kforcone
closed
3 years ago
2
Fix gff empty gene
#44
gamcil
closed
3 years ago
0
add default values to arguments, example usage to help
#43
gamcil
closed
3 years ago
0
Fix `format_links` writing query instead of target name in target column
#42
althonos
closed
3 years ago
1
Examples in help
#41
alegione
closed
3 years ago
3
update citation
#40
gamcil
closed
3 years ago
0
Example GFF files
#39
BenAuxier
closed
3 years ago
4
Feature request: cluster granularity settings
#38
RvV1979
opened
3 years ago
0
Feature request: categorial color scheme for cluster groups
#37
RvV1979
opened
3 years ago
0
Feature request: setting sequence window
#36
RvV1979
closed
3 years ago
3
Issue with multi-exon genes
#35
RvV1979
opened
3 years ago
0
Error raised by low-homology references (ValueError: No alignments are stored in the aligner)
#34
sminot
closed
3 years ago
3
Addition to help text: Double click flips contig
#33
passdan
closed
3 years ago
2
Feature request(s) - On-gene label, autosource group names, legend titles editing, support for manually adding text boxes
#32
UriNeri
opened
3 years ago
4
Add info for conda install
#31
rpetit3
closed
3 years ago
1
How to adjust the distance between the sample name and the sequence in clinker?
#30
jeep3
closed
3 years ago
2
Bioconda submission naming
#29
rpetit3
closed
3 years ago
2
Issue with anaconda3 on mac and Clinker
#28
lgannon248
closed
3 years ago
3
How can I get GTF files into this type of software
#27
bioinfowheat
closed
3 years ago
8
Possible errors when running clinker v0.0.11 with GenBank files from MiBIG
#26
fjell-dev
closed
3 years ago
4
Feature request: match gene order
#25
alexweisberg
closed
3 years ago
4
Add GFF3+FASTA parser
#24
gamcil
closed
3 years ago
0
Link lines, unscaled genes
#23
gamcil
closed
3 years ago
0
Implement parallel computing of alignments
#22
althonos
closed
3 years ago
4
prohibitively slow performance
#21
marade
opened
3 years ago
9
pip install clinker - ERROR: Command errored out with exit status 1
#20
mafeeney
closed
3 years ago
2
pip3 install clinker instead pip install - Ubuntu 20.04 LTS
#19
ghost
closed
3 years ago
1
Refactor globaligner
#18
gamcil
closed
3 years ago
0
Possible to ignore coordinates and show gene order only?
#17
RvV1979
closed
3 years ago
7
fix divide-by-zero when creating matrix with empty alignments
#16
gamcil
closed
3 years ago
0
Possible to add phylogeny to clinker output plot?
#15
jelber2
closed
3 years ago
8
ValueError: Distance matrix 'X' must be symmetric
#14
kforcone
closed
3 years ago
4
check for pseudogenes when parsing SeqFeature objects
#13
gamcil
closed
3 years ago
0
Add --no_align argument
#12
gamcil
closed
3 years ago
0
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