issues
search
jbloomlab
/
SARS2-mut-fitness
Observed substitution counts of SARS-CoV-2 compared to those expected under the mutation rates
MIT License
19
stars
5
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
add `gisaid_2024-04-24` dataset
#50
jbloom
closed
4 months ago
0
Add `public_2024-04-19` dataset
#49
jbloom
closed
4 months ago
0
Add disclaimer for nsp3 heatmap potentially not working
#48
corneliusroemer
closed
9 months ago
1
NSP3 visualization is broken in some browsers, showing sad face
#47
corneliusroemer
opened
9 months ago
3
add `public_2023-10-01` dataset
#46
jbloom
closed
11 months ago
0
Add dms-viz link to README.md
#45
WillHannon-MCB
opened
12 months ago
0
Update `dms-viz` visualization
#44
WillHannon-MCB
closed
12 months ago
2
Add `dms-viz` configuration to the pipeline
#43
WillHannon-MCB
closed
1 year ago
1
manuscript formatted for final Virus Evolution submission
#42
jbloom
closed
1 year ago
0
edit: change last third to last 5kb
#41
rneher
closed
1 year ago
0
paper revisions for Virus Evolution
#40
jbloom
closed
1 year ago
0
Update to 2023-06-21
#39
jbloom
closed
1 year ago
0
Export fitness as a `JSON` file
#38
WillHannon-MCB
closed
1 year ago
3
Richard Neher final edits
#37
jbloom
closed
1 year ago
0
revision of paper based on initial reviews
#36
jbloom
closed
1 year ago
0
fix nsp numbering in `clade_fixed_muts`
#35
jbloom
closed
1 year ago
0
add comparison to other studies estimating mutational effects
#34
jbloom
closed
1 year ago
0
correlate dN/dS values with site estimated fitnesses and DMS
#33
jbloom
closed
1 year ago
0
make version of mutation effects ordered by gene position
#32
jbloom
closed
1 year ago
0
compare to new Flynn 2023 Mpro DMS
#31
jbloom
closed
1 year ago
0
integration synonymous plot script into pipeline better
#30
jbloom
closed
1 year ago
0
Feat/synmuts additions
#29
rneher
closed
1 year ago
0
add `public_2023-05-11` dataset
#28
jbloom
closed
1 year ago
0
Known conserved noncoding
#27
rneher
closed
1 year ago
0
fix bug dropping noncoding counts and calculate nt fitness
#26
jbloom
closed
1 year ago
0
add nucleotide mutation fitness estimates
#25
jbloom
closed
1 year ago
0
noncoding mutations now included in actual versus expected counts
#24
jbloom
closed
1 year ago
0
enable multiple mutation-annotated trees (datasets)
#23
jbloom
closed
1 year ago
0
include estimates for ORF9b
#22
jbloom
closed
1 year ago
0
ORF9b addition
#21
zach-hensel
closed
1 year ago
4
how maintainable is current pipeline and do we care?
#20
jbloom
opened
1 year ago
0
maintaining list of sites to exclude if mutation-annotated tree is updated
#19
jbloom
opened
1 year ago
0
some (final?) tweaks to paper
#18
jbloom
closed
1 year ago
0
Richard edits
#17
jbloom
closed
1 year ago
0
updates to paper
#16
jbloom
closed
1 year ago
0
add comparison to DCA estimates
#15
jbloom
closed
1 year ago
0
add log number of descendants to non-terminal/terminal counts correlation plot
#14
jbloom
closed
1 year ago
0
paper draft
#13
jbloom
closed
1 year ago
0
add references and small edits to paper.tex
#12
jbloom
closed
1 year ago
0
plot average counts per site for each mutation type
#11
jbloom
closed
1 year ago
0
Richard's notes on calculations
#10
jbloom
closed
1 year ago
0
format legends for interactive GitHub pages plots in `./docs/`
#9
jbloom
closed
1 year ago
0
fitness effects versus ratio of non-terminal to terminal branch counts
#8
jbloom
closed
1 year ago
0
add analysis of effects of mutations fixed in clades
#7
jbloom
closed
1 year ago
0
exclude sites masked in pre-built `UShER` tree
#6
jbloom
closed
1 year ago
0
correlate with DMS datasets
#5
jbloom
closed
1 year ago
0
check T95I mutation in Delta clades
#4
jbloom
closed
1 year ago
2
resolve discrepancies with Neher method
#3
jbloom
closed
1 year ago
2
my initial commit
#1
jbloom
closed
1 year ago
0