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jbloomlab
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SARS-CoV-2-RBD_DMS
Deep mutational scanning of the receptor-binding domain of SARS-CoV-2 Spike
BSD 3-Clause "New" or "Revised" License
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Update circulating variants nb
#52
tylernstarr
closed
4 years ago
0
Update single mut nb
#51
tylernstarr
closed
4 years ago
0
Homolog validation figures
#50
tylernstarr
closed
4 years ago
0
Update antibody epitopes md
#49
tylernstarr
closed
4 years ago
0
Isogenic titrations
#48
ajgreaney
closed
4 years ago
0
Update sarbecovirus diversity nb
#47
tylernstarr
closed
4 years ago
0
Update analyses
#46
tylernstarr
closed
4 years ago
0
Sarbecovirus diversity
#45
tylernstarr
closed
4 years ago
0
Update validations
#44
tylernstarr
closed
4 years ago
0
Antibody epitopes
#43
tylernstarr
closed
4 years ago
0
Circulating variants
#42
tylernstarr
closed
4 years ago
0
Tweak and rerun single_mut_effects
#41
tylernstarr
closed
4 years ago
0
Structure function
#40
tylernstarr
closed
4 years ago
1
clean run of pipeline
#39
jbloom
closed
4 years ago
0
Fresh run
#38
tylernstarr
closed
4 years ago
0
Track key data files
#37
jbloom
closed
4 years ago
0
Improve muteffects output
#36
jbloom
closed
4 years ago
3
Update single mut effects homologs
#35
tylernstarr
closed
4 years ago
0
update `README.md` to describe `R` env / steps
#34
jbloom
closed
4 years ago
0
remove unused scripts / notebooks
#33
jbloom
closed
4 years ago
0
Final mut effects
#32
tylernstarr
closed
4 years ago
1
Fit isogenic titrations
#31
tylernstarr
closed
4 years ago
0
Update structural annotation
#30
tylernstarr
closed
4 years ago
2
Add lib2 s4 b3
#29
tylernstarr
closed
4 years ago
1
add MiSeq data to barcode_runs.csv
#28
tylernstarr
closed
4 years ago
11
Compute binding and expression scores, and fit global epistasis models
#27
tylernstarr
closed
4 years ago
0
Re-run updated analyze_counts_expression_Sortseq
#26
tylernstarr
closed
4 years ago
0
Run first draft of biniding functional scores computation
#25
tylernstarr
closed
4 years ago
0
Update notebook to calculate expression scores, generate .md summary
#24
tylernstarr
closed
4 years ago
1
Rerun pipeline from start
#23
tylernstarr
closed
4 years ago
1
add `analyze_counts` notebook
#22
jbloom
closed
4 years ago
1
Modify analyze_counts_expression_Sortseq script
#21
tylernstarr
closed
4 years ago
1
Update sample names
#20
tylernstarr
closed
4 years ago
0
parse barcodes more effectively, get `Snakefile` working
#19
jbloom
closed
4 years ago
1
Add HKU3-1
#18
tylernstarr
closed
4 years ago
0
count variants with multiple targets
#17
jbloom
closed
4 years ago
3
cleaner names for barcode runs
#16
jbloom
closed
4 years ago
2
fix barcode run Illumina locations
#15
jbloom
closed
4 years ago
1
Update data inputs
#14
tylernstarr
closed
4 years ago
0
Add pointers to Illumina runs and metadata about bin samples
#13
tylernstarr
closed
4 years ago
0
Update dssp call
#12
tylernstarr
closed
4 years ago
1
build the variants
#11
jbloom
closed
4 years ago
0
successfully run `process_ccs` for multiple targets
#10
jbloom
closed
4 years ago
1
run `ccs` on PacBio samples
#9
jbloom
closed
4 years ago
1
Add pointer to last of the four PacBio reads
#8
tylernstarr
closed
4 years ago
0
Add pointers to first three of four PacBio raw data
#7
tylernstarr
closed
4 years ago
0
fix plotting of targets in `process_ccs.ipynb`
#6
jbloom
closed
4 years ago
1
set up to analyze multiple PacBio amplicons
#5
jbloom
closed
4 years ago
2
install `dssp` into conda environment
#4
jbloom
closed
4 years ago
4
simplify process to set up `conda` environment
#3
jbloom
closed
4 years ago
1
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