andersen-lab Freyja issues

andersen-lab / Freyja

Depth-weighted De-Mixing

BSD 2-Clause "Simplified" License

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pyarrow missing from conda environment in v1.5.1

#244 ktmeaton closed 4 days ago
3
Demix hierarchy output path

#243 mariaelf97 opened 1 week ago
0
Solver options

#242 joshuailevy closed 3 weeks ago
0
Breaking out novel variants given BA.2.86 evolution

#241 andrew-rothstein closed 3 weeks ago
3
make json format readable

#240 joshuailevy closed 3 weeks ago
0
Switch from barcode formatted as csv to feather and paired json

#239 joshuailevy closed 3 weeks ago
0
ECOS deprecation and increasing frequency of demix errors

#238 ktmeaton closed 3 weeks ago
3
Using --depthcutoff for some recent high coverage genomes

#237 owenssm closed 3 weeks ago
1
[BUG]: barcode version is stuck on 04_30_2024-01-10

#236 erinyoung closed 1 month ago
3
Freyja plot explanation

#235 ChromatinLab opened 2 months ago
2
Freyja plot key is hard to read

#234 nicolegobo closed 3 weeks ago
3
[BUG] Unexpected Behavior Depending on Reference

#233 whottel closed 2 months ago
2
226 freyja covariants fixes

#232 dylanpilz closed 4 weeks ago
0
Raise errors instead of exiting

#231 dylanpilz closed 2 months ago
0
229 random seed boot

#230 mariaelf97 closed 2 months ago
0
Random seed for freyja boot for consistent results

#229 ktmeaton closed 2 months ago
1
Freyja plot error

#228 ChromatinLab opened 2 months ago
5
[BUG] freyja exits rather than raising errors

#227 wutron closed 2 months ago
1
Freyja covariants runtime error

#226 RainerWaldmann closed 4 weeks ago
2
Get lineage def

#225 dylanpilz closed 3 months ago
0
Sphinx docs

#224 dylanpilz closed 3 months ago
0
Variant threshold

#223 mariaelf97 closed 3 months ago
0
Variant threshold

#222 mariaelf97 closed 3 months ago
0
clarification about the result

#221 Petrichor-sudo closed 3 weeks ago
4
Lineage specific plot trouble shooting

#220 Aishah86 opened 3 months ago
3
Collapse updates

#219 joshuailevy closed 3 months ago
0
Create issue templates

#218 dylanpilz closed 4 months ago
0
cvxpy.error.SolverError: Solver 'ECOS' failed

#217 EricFournier3 closed 3 months ago
10
The purpose of providing reference genomes file, and Demixing error

#216 Petrichor-sudo closed 3 months ago
1
AttributeError: 'Series' object has no attribute 'columns'

#215 jchorl opened 4 months ago
0
Restructuring imports, show defaults via CLI help

#214 joshuailevy closed 4 months ago
0
-like lineages grouped within "Other" VOC

#213 ktmeaton closed 3 months ago
4
Clarify difference between `--covcut` and `--depthcutoff`

#212 tavareshugo opened 4 months ago
2
Improve documentation with default values used

#211 tavareshugo closed 4 months ago
1
Some problem about the UshER barcodes output

#210 Bin-Ma closed 3 months ago
1
Dash and plotting modifications

#209 joshuailevy closed 4 months ago
0
freyja demix error citing insufficient sequencing depth

#208 michellescribner closed 4 months ago
3
Additional coverage estimates, minor fixes

#207 dylanpilz closed 5 months ago
0
freyja boot error messages missing in output

#206 ktmeaton closed 5 months ago
2
Is there a risk that freyja recover the wrong XDD relative lineage abundances?

#205 Fuyulinn closed 5 months ago
2
165 lineage file

#204 mariaelf97 closed 4 months ago
0
Freyja plot failures with low-coverage samples

#203 kevinlibuit closed 5 months ago
2
Spike coverage estimates

#202 joshuailevy closed 5 months ago
0
ECOS problem reopening not due to low sample coverage but update

#201 CeliaRodrigues closed 5 months ago
12
Requesting help with understanding and usage of `--confirmedonly` flag

#200 NickD-BHSc closed 5 months ago
2
Solve #188

#199 joshuailevy closed 5 months ago
1
Issue fixes

#198 joshuailevy closed 5 months ago
0
Wrong lineages?

#197 LauraVP1994 closed 3 weeks ago
1
Freyja plot help

#196 ADY-PANDA closed 3 months ago
8
Add option to retain intermediate figure outputs

#195 jchorl closed 5 months ago
4