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VIB-PSB
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ksrates
ksrates is a tool to position whole-genome duplications relative to speciation events using substitution-rate-adjusted mixed paralog-ortholog Ks distributions.
https://ksrates.readthedocs.io
GNU General Public License v3.0
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Update Dockerfile and GitHub workflow to push container
#61
Cecilia-Sensalari
opened
2 months ago
0
Add support for Read the Docs v2
#60
Cecilia-Sensalari
closed
5 months ago
0
Difficulty in Output Plots Interpretation
#59
abcbot123
closed
5 months ago
3
Fix version number 1.1.4 in __version__
#58
Cecilia-Sensalari
closed
5 months ago
0
Updated Errors
#57
zhouxp9709
closed
5 months ago
11
No output files
#56
abcbot123
opened
6 months ago
17
Installation problem
#55
majssssa
closed
5 months ago
11
where would I find the equation or lognorm fit parameters to the Ks distributions?
#54
tamsen
opened
8 months ago
10
ortholog_peak_db.tsv, ortholog_ks_list_db.tsv database are not generated
#53
B10inform
closed
9 months ago
2
ERROR Unexpected internal error during analysis of gene family GF_000001
#52
jwang147
closed
1 year ago
2
Supporting new Nextflow DSL2 syntax
#51
Cecilia-Sensalari
opened
1 year ago
0
Bugfix for exponential-lognormal mixture model: remove weight rounding during EM iterations
#50
Cecilia-Sensalari
closed
1 year ago
0
Add warning for negative distances during rate-adjustment
#49
Cecilia-Sensalari
closed
1 year ago
0
ERROR Unexpected internal error during analysis of gene family GF_000001
#48
jwang147
closed
1 year ago
4
ksrates paralogs-ks seemingly freezing on i-adhore step
#47
sjfleck
closed
1 year ago
9
Avoid exiting due to i-ADHoRe warnings
#46
Cecilia-Sensalari
closed
1 year ago
0
Warning: Dubious indirect gene relationship - closest genes get same color in alignment
#45
sjfleck
closed
1 year ago
2
installation error
#44
sjfleck
closed
1 year ago
2
Add support for Nextflow version 22.03.0-edge and later
#43
Cecilia-Sensalari
closed
2 years ago
0
TypeError: cannot convert the series to <class 'float'>
#42
Biscuite-wzy
closed
2 years ago
10
Issue with wgd paralog Ks analysis
#41
caiobrunharo
closed
2 years ago
4
singularity
#40
major-one
closed
2 years ago
5
Incompatibility with recent Nextflow version
#39
Cecilia-Sensalari
closed
2 years ago
4
Error when executing ksrates test in nextflow
#38
dawickell
closed
2 years ago
5
User-defined filename/path for expert config file
#37
Cecilia-Sensalari
closed
2 years ago
0
Improve checkpoint for divergence colors provided in configuration file
#36
Cecilia-Sensalari
closed
2 years ago
0
Check Newick tree structural integrity
#35
Cecilia-Sensalari
closed
2 years ago
0
Fix test GitHub action
#34
Cecilia-Sensalari
closed
2 years ago
0
Add CITATION.cff
#33
Cecilia-Sensalari
closed
2 years ago
0
Update requirement.txt with module versions
#32
Cecilia-Sensalari
closed
2 years ago
0
Update push GitHub action to support ARM
#31
Cecilia-Sensalari
closed
2 years ago
0
Use buildx to have ARM architecture
#30
Cecilia-Sensalari
closed
2 years ago
0
Automate version update
#29
Cecilia-Sensalari
closed
2 years ago
0
Fix: plot-paralogs command generates directory if needed
#28
Cecilia-Sensalari
closed
2 years ago
0
Rename "correction" to "adjustment" in doc-strings and logging
#27
Cecilia-Sensalari
closed
2 years ago
0
A tree with branch length set to "rate-adjusted mixed Ks distances" and its Newick string?
#26
goshng
closed
2 years ago
1
Condense, improve and clean up Nextflow logging
#25
lohausr
closed
3 years ago
0
LMM skipped if components are more than datapoints
#24
Cecilia-Sensalari
closed
3 years ago
0
Nextflow pipeline removes leftover folders/files
#23
Cecilia-Sensalari
closed
3 years ago
10
Update Usage docs (iterative ksrates runs)
#22
Cecilia-Sensalari
closed
3 years ago
0
Improve compatibility between pipeline & cluster
#21
Cecilia-Sensalari
closed
3 years ago
4
Increase memory for paralogsAnalyses NF process
#20
Cecilia-Sensalari
closed
3 years ago
0
Add compact custom-made Nextflow error report
#19
Cecilia-Sensalari
closed
3 years ago
2
Nextflow config update (autoMounts, envWhitelist)
#18
Cecilia-Sensalari
closed
3 years ago
1
Rename parameters in configuration file
#17
Cecilia-Sensalari
closed
3 years ago
0
Docs: interactive containers and WSL2 notes
#16
Cecilia-Sensalari
closed
3 years ago
0
Reorder local installation steps in documentation
#15
Cecilia-Sensalari
closed
3 years ago
0
Rename and describe headers in output files
#14
Cecilia-Sensalari
closed
3 years ago
0
Fix dark gray color of anchor pair KDE
#13
Cecilia-Sensalari
closed
3 years ago
0
Legend of ELMM models has handle pairs (tuples)
#12
Cecilia-Sensalari
closed
3 years ago
0
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