issues
search
blab
/
cartography
Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2
https://doi.org/10.1101/2024.02.07.579374
MIT License
4
stars
1
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Finalize cartography manuscript revisions
#127
huddlej
opened
6 days ago
0
Clarify robustness of methods to homoplasies, reversions, and missing data
#126
huddlej
closed
5 days ago
0
Use pathogen cluster mutations command
#125
huddlej
closed
4 days ago
0
Refine figure aesthetics
#124
huddlej
closed
1 week ago
0
Evaluate within-clade t-SNE cluster accuracy for SARS-CoV-2
#123
huddlej
closed
1 week ago
0
Process HA and NA alignments separately
#122
huddlej
closed
2 weeks ago
1
Run HA/NA analysis with separate distance matrices for HA and NA
#121
huddlej
closed
2 weeks ago
1
Update coronavirus like simulation generations
#120
huddlej
closed
4 weeks ago
0
Run HDBSCAN directly on genetic distances and compare clusters to those from embeddings
#119
huddlej
closed
2 weeks ago
0
Rerun coronavirus simulations with the same number of years as influenza
#118
huddlej
closed
4 weeks ago
0
Text edits
#117
huddlej
closed
1 month ago
0
Rerun PCA with simplex encoding of sequences
#116
huddlej
closed
1 month ago
0
Rerun all PCA and t-SNE analyses with alternate encoding of inputs for PCA
#115
huddlej
closed
1 month ago
0
Report IQ-TREE parameters in methods
#114
huddlej
closed
1 month ago
0
Add description of how we plan to use these methods for specific use cases like outbreak response
#113
huddlej
closed
1 month ago
0
Compare number of cluster-specific mutations to the number of clade-specific mutations
#112
huddlej
closed
4 days ago
0
Consider defining a metric of cluster confidence based on the number of cluster-specific mutations
#111
huddlej
closed
4 days ago
0
Assess cluster accuracy compared to Pango lineages for embeddings within a specific SC2 clade
#110
huddlej
closed
1 week ago
0
Clarify value of including additional gene segments beyond HA/NA for influenza embeddings
#109
huddlej
closed
1 month ago
0
Add supplemental figure(s) that shows tangletree from Nextstrain between HA and NA colored by MCC and/or t-SNE clusters
#108
huddlej
closed
1 week ago
0
Clarify sensitivity of methods to homoplasies, reversions, etc. and confidence metrics for clusters
#107
huddlej
closed
5 days ago
0
Attempt plotting with rectangular tree layout in Altair
#106
huddlej
closed
1 week ago
0
Remove variable branch widths from tree and embedding figures
#105
huddlej
closed
1 week ago
0
Cite related network/cluster-based visualization approaches (e.g., MicrobeTrace)
#104
huddlej
closed
1 month ago
0
Elaborate on contents of supplemental figures and tables in their captions
#103
huddlej
closed
1 month ago
0
Expand description of simulated populations in results
#102
huddlej
closed
1 month ago
0
Link to supplemental data files on Zenodo from each supplemental item's caption
#101
huddlej
closed
1 month ago
0
Test interpretability of tree/embedding figures with alternate color schemes
#100
huddlej
closed
1 week ago
0
Run HDBSCAN directly on genetic distances and compare clusters to those from embeddings
#99
huddlej
closed
2 weeks ago
0
Update preprint files
#98
huddlej
opened
4 months ago
0
Update cover letter
#97
huddlej
closed
3 months ago
0
Update LaTeX template
#96
huddlej
closed
3 months ago
0
Cite additional related work
#95
huddlej
closed
4 months ago
1
Report how methods scale with data size
#94
huddlej
closed
4 months ago
0
Clarify novelty of main results in abstract, intro, results, and discussion
#93
huddlej
closed
4 months ago
0
Add supplemental figures with cluster vs. genetic group heatmap
#92
huddlej
closed
4 months ago
0
Add supplemental figures of example SARS-CoV-2 recombination events visualized with MDS
#91
huddlej
closed
3 months ago
0
Add headers to the discussion
#90
huddlej
closed
4 months ago
0
Fix boxplot positions to allow gaps between genetic distances on the x-axis
#89
huddlej
closed
4 months ago
0
Reduce verbosity of the results
#88
huddlej
closed
6 months ago
0
Reduce verbosity of results
#87
huddlej
closed
6 months ago
0
Address inadequate justification for optimization metrics of linearity and cluster accuracy
#86
huddlej
closed
6 months ago
0
Address lack of prescriptive settings for methods applied to new viruses
#85
huddlej
closed
6 months ago
0
Cover letter
#84
huddlej
closed
7 months ago
1
Quantify monophyletic clusters
#83
huddlej
closed
7 months ago
0
Determine the effect of sampling bias (e.g., regional or clade composition bias) on embeddings and cluster accuracy
#82
huddlej
closed
7 months ago
0
Automate recombinant lineages
#81
huddlej
closed
7 months ago
0
Calculate branch positions for internal nodes
#80
huddlej
closed
7 months ago
0
Quantify monophyly of clusters for early/late flu and early SC2 by counting the number of ancestral state switches for each cluster when traversing the tree in preorder
#79
huddlej
closed
7 months ago
0
Plot embeddings by clade with branches from the phylogeny for early and late H3N2 HA and early SC2 to show how embeddings correspond to phylogeny
#78
huddlej
closed
7 months ago
0
Next