PoonLab vindels issues - Githubissues

PoonLab / vindels

Developing an empirical model of sequence insertion and deletion in virus genomes

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Missing data set

#103 ArtPoon opened 1 year ago
0
9_5_indel_rates.r - Error: $ operator is invalid for atomic vectors

#102 ArtPoon closed 1 year ago
3
9_5_indel_rates.r: iTotal has no variable pat

#101 ArtPoon closed 2 years ago
2
Input is data.frame but should be a plain list of items to be stacked

#100 ArtPoon closed 1 year ago
0
Additional Nucleotide Figures

#99 jpalmer37 closed 1 year ago
0
Historian sanity checks

#98 jpalmer37 closed 3 years ago
2
Indel rate analysis using standard R GLM

#97 jpalmer37 closed 3 years ago
1
Investigating convergence for RStan indel rate analyses

#96 jpalmer37 closed 4 years ago
1
Clean up slippage model/template switching model MCMC sampling code

#95 ArtPoon closed 3 years ago
4
Convert within-host thesis chapter to paper

#94 ArtPoon closed 1 year ago
1
Resolve underestimation of confidence intervals from RStan

#93 ArtPoon closed 4 years ago
1
Comparing tree sampling BEAST runs to constrained runs

#92 ArtPoon closed 3 years ago
1
Slip Model - Fixation parameter of non3s

#91 jpalmer37 closed 4 years ago
2
Determine best layout for indel lengths

#90 jpalmer37 closed 4 years ago
0
Determine final set of figures

#89 jpalmer37 closed 4 years ago
3
Check whether variable loops lengthen/shrink over time

#88 jpalmer37 closed 4 years ago
2
Fit slippage model to insertions data set

#87 ArtPoon closed 4 years ago
3
Running too many threads on BEVi, unable to log in

#86 jpalmer37 closed 5 years ago
1
Clock rate not exploring parameter space

#85 jpalmer37 closed 5 years ago
7
RAPR has a limit of 800 sequences

#84 jpalmer37 closed 5 years ago
1
Hypermut removed very large portion of sequences from dataset

#83 jpalmer37 closed 5 years ago
3
Handling superinfection cases

#82 ArtPoon closed 5 years ago
5
Review literature for patient data sets

#81 ArtPoon closed 4 years ago
2
Insertions / Deletions Affecting N-glyc sites

#80 jpalmer37 closed 4 years ago
4
Diagnosing temporal signal

#79 jpalmer37 closed 5 years ago
1
Skygrid tree priors fail on the cluster, not Lio

#78 jpalmer37 closed 5 years ago
1
Check data sources

#77 ArtPoon closed 5 years ago
3
Fragmented deletions

#76 jpalmer37 closed 5 years ago
2
Flanking insertion sequences

#75 jpalmer37 closed 4 years ago
12
Acute / chronic N-glyc sites

#74 jpalmer37 closed 5 years ago
8
BEAST runs stopping due to errors

#73 jpalmer37 closed 5 years ago
4
Hypothesis Testing - Dinucleotide Proportions

#72 jpalmer37 closed 5 years ago
4
Handling data sets that failed BEAST analysis

#71 jpalmer37 closed 5 years ago
6
Problem with MPI script running Historian on cluster

#70 ArtPoon closed 4 years ago
3
Do some model comparison in BEAST

#69 ArtPoon closed 4 years ago
4
sudo access on BEVi

#68 jpalmer37 closed 5 years ago
2
Insertion/Deletion Rates (20 tree samples)

#67 jpalmer37 closed 5 years ago
0
Cherry Genetic Distances

#66 jpalmer37 closed 5 years ago
4
Check whether Novitsky data is already included

#65 ArtPoon closed 5 years ago
1
Some alignments contain many more than 100 sequences

#64 ArtPoon closed 5 years ago
1
EDA within host insertions

#63 jpalmer37 closed 5 years ago
19
GeoPIP works on test files, but not my own

#62 jpalmer37 closed 5 years ago
0
Sampling Trees

#61 jpalmer37 closed 5 years ago
0
Thin log file so that step numbers match tree log

#60 ArtPoon closed 5 years ago
1
MBE editors and reviewers

#59 ArtPoon closed 5 years ago
2
Beauti.py Reading Error

#58 jpalmer37 closed 5 years ago
10
BEAST Parameters

#57 jpalmer37 closed 5 years ago
1
Withinhost MSAs and Trees

#56 jpalmer37 closed 5 years ago
0
GLM N-glycosylation sites

#55 jpalmer37 closed 5 years ago
11
Different outputs obtained from different GLM references

#54 jpalmer37 closed 5 years ago
2