jbloomlab seqneut-pipeline issues

jbloomlab / seqneut-pipeline

Pipeline for analyzing sequencing-based neutralization assays

MIT License

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Snakemake does not support mamba

#53 anloes closed 1 month ago
1
remove `defaults` from `conda` envs

#52 jbloom closed 1 month ago
2
update citation to Loes 2024 JVI paper

#51 jbloom closed 1 month ago
0
Update manualdrops to allow to specify serum_replicates to exclude

#50 anloes closed 2 months ago
1
plate-level manual drops with 'serum-replicates' causes assertion error, same error as seen in #45

#49 anloes closed 2 months ago
1
update README to link to new Bloom lab webpage

#48 jbloom closed 2 months ago
0
Update README.md

#47 anloes closed 6 months ago
0
specify counts columns in manual_drops

#46 ckikawa closed 6 months ago
4
plate-level manual drops with 'wells' causes assertion error

#45 ckikawa closed 6 months ago
4
enable plate-level indices as `upstream2` in barcode parsing

#44 jbloom closed 7 months ago
0
plot curves with `draw_in_bounds` so line does not go past points

#43 jbloom closed 7 months ago
0
update software versions

#42 jbloom closed 7 months ago
0
adjust suggested range for `fixslope` in test example

#41 jbloom closed 7 months ago
0
Adding code for processing read 1, plate based indexing

#40 anloes closed 7 months ago
5
categorize plates by group

#39 jbloom closed 7 months ago
0
report titers out of bounds of dilution series

#38 jbloom closed 7 months ago
0
goodness of fit looks at both RMSD and R2

#37 jbloom closed 7 months ago
0
reasonable suggestions for `fixslope` range for example / docs

#36 jbloom closed 7 months ago
2
parameters can now be constrained in range (`fixtop`, `fixbottom`, `fixslope`)

#35 jbloom closed 7 months ago
0
update env to `neutcurve` 2.0.0

#34 jbloom closed 7 months ago
0
improve goodness of fit assessments

#33 jbloom closed 7 months ago
1
enable constraints on parameter ranges

#32 jbloom closed 7 months ago
1
allow plates and sera to be categorized into groups

#31 jbloom closed 7 months ago
2
Include a mechanism to indicate that titers that are estimated to be out of bounds in summary plots

#30 anloes closed 7 months ago
1
add citation to Loes 2024 to README

#29 jbloom closed 8 months ago
0
add option to specify additional HTMLs in docs

#28 jbloom closed 8 months ago
0
add `miscellaneous_plates` to count barcodes for additonal plates

#27 jbloom closed 9 months ago
0
add `miscellaneous_plates` to configuration YAML

#26 jbloom closed 9 months ago
0
update to `dms_variants` 1.5.0

#25 jbloom closed 9 months ago
0
update dms_variants version

#24 ckikawa closed 9 months ago
1
final tweaks and bug fixes for version 2.0.0

#23 jbloom closed 10 months ago
0
aggregate and plot QC failures

#22 jbloom closed 10 months ago
0
Refactor `serum_titers` rule to automate QC

#21 jbloom closed 10 months ago
0
re-factor processing of plates to `process_plates` rule

#20 jbloom closed 10 months ago
0
update to `neutcurve` 1.0 and `snakemake` 8.0

#19 jbloom closed 10 months ago
0
Update filtering for max fraction infectivity and for curves where midpoint is substantially different from nt50

#18 anloes closed 10 months ago
4
Max fraction infectivity filter and barcode fraction consistency filter should be moved from plate QC to curve fitting QC

#17 anloes closed 10 months ago
1
The data which indicates that samples should be removed due to QC issues is removed when filtering is done from the config.yml

#16 anloes closed 10 months ago
1
Add mechanism to drop single serum sample from a given plate

#15 anloes closed 10 months ago
1
handle QC of sera

#14 jbloom closed 9 months ago
2
add `min_frac_infectivity` filter

#13 jbloom closed 11 months ago
0
fix `snakemake` params re-run triggers

#12 jbloom closed 11 months ago
0
fix docs links

#11 jbloom closed 11 months ago
0
add `docs` to render on GitHub Pages

#10 jbloom closed 11 months ago
0
test titers are as expected

#9 jbloom closed 11 months ago
0
aggregate titers across sera

#8 jbloom closed 11 months ago
0
add `serum_titers` rule

#7 jbloom closed 11 months ago
0
add automated tests and lint / format code

#6 jbloom closed 11 months ago
0
add `test_example`

#5 jbloom closed 11 months ago
0
pipeline now fits and plots neutralization curves for each plate

#4 jbloom closed 11 months ago
0