microbial-pangenomes-lab microGWAS issues

microbial-pangenomes-lab / microGWAS

Bacterial GWAS analysis

https://microgwas.readthedocs.io

MIT License

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issues

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fix params

#55 jburgaya closed 1 month ago
0
Some changes to the tutorial page

#54 mgalardini closed 1 month ago
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Modified documentation

#53 Bamu-d closed 1 month ago
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improved params section

#52 jburgaya closed 1 month ago
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made generalised scripts for zoommed in and volcano plots

#51 Bamu-d closed 1 month ago
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add length, minhits, maxgenes as params

#50 jburgaya closed 1 month ago
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Directly integrate downloading eggnog DB into the workflow

#49 mgalardini closed 1 month ago
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modified tutorials for documentation

#48 Bamu-d closed 1 month ago
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modified documentation to include a tutorial section and reviews sugg…

#47 Bamu-d closed 2 months ago
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Generate the QQ plot for panfeed also

#46 mgalardini closed 2 months ago
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Change color scale for enrichment plots

#45 mgalardini closed 2 months ago
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Forgot to add the 'strain' column

#44 mgalardini closed 2 months ago
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Eggnog

#43 jburgaya closed 2 months ago
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Update README.md

#42 jburgaya closed 2 months ago
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Skip the second pass of panfeed for annotate_summary

#41 mgalardini closed 2 months ago
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Choice of reference genomes

#40 LudoPoire closed 2 months ago
3
VCFs as input

#39 GaloGS closed 2 months ago
2
Update README.md

#38 mgalardini closed 4 months ago
0
Update conf.py

#37 mgalardini closed 4 months ago
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Fix problems with glmnet_python

#36 mgalardini closed 4 months ago
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Update usage.rst

#35 mgalardini closed 4 months ago
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Update README.md

#34 mgalardini closed 4 months ago
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Omit terms with zero gene counts from the plot

#33 Bamu-d closed 4 months ago
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minor edit

#32 jburgaya closed 4 months ago
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QQ plots for panfeed associations

#31 jburgaya closed 2 months ago
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minor fix plots labels

#30 jburgaya closed 4 months ago
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Avoid potential conflicts between concurrent runs of map_back

#29 mgalardini closed 4 months ago
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Make the tracking actually work

#28 mgalardini closed 4 months ago
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Add tracking to docs page (simple analytics)

#27 mgalardini closed 4 months ago
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Fix readthedocs build

#26 mgalardini closed 4 months ago
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Update README.md

#25 jburgaya closed 4 months ago
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Update README.md

#24 jburgaya closed 4 months ago
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minor fix

#23 jburgaya closed 5 months ago
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First draft of the documentation

#22 mgalardini closed 4 months ago
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Remove a ugly hack in panfeed rule

#21 mgalardini closed 5 months ago
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Generate plots and enrichments for panfeed and allow for covariates

#20 mgalardini closed 5 months ago
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Add abritamr to the tests and in the suggested snakemake cmd

#19 mgalardini closed 5 months ago
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deleted_uniref50_instruction

#18 JennyFiebig closed 5 months ago
0
File of files paradigm

#17 mgalardini closed 5 months ago
1
Testing fixes

#16 mgalardini closed 5 months ago
1
Create a test dataset and provide various bugfixes/improvements as a bonus

#15 mgalardini closed 6 months ago
0
abritamr rule

#14 jburgaya closed 6 months ago
0
Update README.md

#13 jburgaya closed 6 months ago
0
functional_enrichment analysis

#12 Bamu-d closed 5 months ago
0
Swap `unitig-counter` for other alternative

#11 jburgaya opened 7 months ago
0
Swap sift4g for more modern alternatives

#10 jburgaya closed 5 months ago
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Use snakemake resources system to budget memory requirements

#9 jburgaya opened 7 months ago
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handle cases in which the reference genome has more than one chromosome

#8 jburgaya opened 7 months ago
0
Add references to the tools used in the pipeline

#7 jburgaya closed 4 months ago
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Combine all annotations in a series of webpages

#6 jburgaya opened 7 months ago
0