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PoonLab
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gromstole
Quantifying SARS-CoV-2 VoCs from NGS data of wastewater samples
MIT License
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Empty output files generated by Freyja
#94
GopiGugan
closed
2 months ago
2
Missing dependency after freyja update
#93
GopiGugan
closed
3 months ago
3
Lab changed column headers in metadata file
#92
ArtPoon
opened
4 months ago
0
Special characters in directory names
#91
GopiGugan
opened
5 months ago
1
Overlapping Freyja Runs
#90
GopiGugan
closed
6 months ago
5
Summary JSON file did not get generated
#89
GopiGugan
closed
5 months ago
3
Maintain a local database of mutation frequencies from gromstole outputs
#88
ArtPoon
opened
8 months ago
4
Outdir not working
#87
LauraVP1994
closed
6 months ago
2
Rerunning one sample from a run removes the summary files for other samples
#86
GopiGugan
closed
5 months ago
1
estimate-freqs.R fails on example data
#85
ArtPoon
closed
1 year ago
7
Lineage removed from usher barcode file
#84
Abayomi-Olabode
closed
1 year ago
2
Script to update Freyja CSV outputs with new LOIs?
#83
ArtPoon
closed
1 year ago
2
Install Freyja on Paphlagon
#82
ArtPoon
closed
1 year ago
3
Estimating confidence intervals for Freyja outputs
#81
ArtPoon
opened
1 year ago
2
Summarizing Freyja outputs
#80
ArtPoon
closed
1 year ago
1
estimate-freqs: error when computing confidence interval
#79
GopiGugan
closed
1 year ago
0
Mutation frequency plots - K417T and R493Q missing recent samples
#78
ArtPoon
closed
1 year ago
1
Compare Freyja outputs with Gromstole
#77
ArtPoon
closed
1 year ago
2
Modify estimate-freqs to use nucleotide substitutions
#76
GopiGugan
closed
1 year ago
2
Need to update mutation lists for several other lineages
#75
ArtPoon
closed
1 year ago
6
Unsupported date format in recent sample
#74
ArtPoon
closed
1 year ago
1
Revisit BQ.1.1 mutation list
#73
ArtPoon
closed
1 year ago
7
collate-mapped.py failing to match Western samples to metadata
#72
ArtPoon
closed
1 year ago
5
Need to modify estimate-freqs to use nucleotide substitutions
#71
ArtPoon
closed
1 year ago
12
Run name mismatch between uploads and results folders
#70
ArtPoon
closed
1 year ago
3
Make interactive plot of mutation frequencies
#69
ArtPoon
closed
1 year ago
1
Make mutation list for BQ.1?
#68
ArtPoon
closed
1 year ago
6
Double-check BA.2.75 estimates
#67
ArtPoon
closed
2 years ago
2
Empty mapped files
#66
GopiGugan
closed
2 years ago
3
Eliminate overlap between BA.2 and BA.5 frequency estimates
#65
ArtPoon
closed
2 years ago
6
Implement basic e-mail notification system to track pipeline runs, exceptions
#64
ArtPoon
closed
2 years ago
0
Versioning
#63
ArtPoon
closed
1 year ago
0
Western latest result lacking summary files
#62
Abayomi-Olabode
closed
2 years ago
2
BA.2.75
#61
ArtPoon
closed
2 years ago
4
Check for N:D377Y in samples
#60
ArtPoon
closed
2 years ago
0
make-barplots: need finite 'ylim' values
#59
ArtPoon
closed
2 years ago
6
Concurrent Runs / Run while data files are being uploaded
#58
GopiGugan
opened
2 years ago
5
Zero counts for C26060T and aa:orf6:D61L for BA.2 samples
#57
ArtPoon
closed
2 years ago
4
Parse mutation function in seq_utils failing to handle codons containing 'Ns'
#56
Abayomi-Olabode
closed
2 years ago
1
Errors when running the estimate-freqs script
#55
GopiGugan
closed
1 year ago
27
Large numbers of failed samples in a Waterloo run
#54
ArtPoon
closed
2 years ago
14
Determine why some samples have high frequencies of both BA.1 and BA.2 that sum >100%
#53
ArtPoon
closed
2 years ago
11
Check for false Delta due to incursion of mutations into Omicron
#52
ArtPoon
closed
2 years ago
6
Update constellations to detect BA.3-BA.5
#51
ArtPoon
closed
2 years ago
5
Iss48
#50
ArtPoon
closed
2 years ago
1
Hierarchical Bayes
#49
ArtPoon
closed
2 years ago
0
Missing variant frequency estimates
#48
ArtPoon
closed
2 years ago
10
Accommodate different primer sets (v3, v4)
#47
ArtPoon
closed
2 years ago
2
estimate-freqs error
#46
suskraem
closed
2 years ago
4
Running viralrecon
#45
Abayomi-Olabode
closed
2 years ago
5
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