zktuong dandelion issues

zktuong / dandelion

dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data

https://sc-dandelion.readthedocs.io/

GNU Affero General Public License v3.0

103 stars 25 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Backports error

#432 obrien-james opened 1 week ago
4
pip prod(deps): update pandas requirement from <=2.2.2,>=1.0.3 to >=1.0.3,<=2.2.3

#431 dependabot[bot] closed 1 week ago
1
pip dev(deps-dev): update sphinx-autodoc-typehints requirement from <=2.2.3 to <=2.4.4

#430 dependabot[bot] closed 1 week ago
1
fix clone_key not respected properly if non-default clone_id

#429 zktuong closed 1 week ago
1
reannotate_genes encountered Unknown argument: "c_region_db" Error and so on

#428 Cscharlotte closed 2 weeks ago
6
pip dev(deps-dev): update sphinx-autodoc-typehints requirement from <=2.2.3 to <=2.4.1

#427 dependabot[bot] closed 1 week ago
1
pip dev(deps-dev): update scirpy requirement from <=0.17.2 to <=0.18.0

#426 dependabot[bot] closed 1 week ago
1
process Parse Biosciences Evercode TCR/BCR files

#425 zktuong opened 3 weeks ago
0
fix downsampling logic in generate network

#424 zktuong closed 2 weeks ago
1
Gene expression scRNA-seq

#423 Jiawei-Xing closed 3 weeks ago
1
pip dev(deps-dev): update sphinx-autodoc-typehints requirement from <=2.2.3 to <=2.4.0

#422 dependabot[bot] closed 2 weeks ago
1
add foldchange test for consensus_count (for check_contigs())

#421 HongjianSun opened 3 weeks ago
1
new saving mode

#420 zktuong closed 3 weeks ago
2
deprecate reliance on `pandas.to_hdf` to save files

#419 zktuong closed 3 weeks ago
1
pin tables version

#418 zktuong closed 3 weeks ago
0
check if tables is failing tests

#417 zktuong closed 4 weeks ago
0
update type hinting

#416 zktuong closed 4 weeks ago
0
Update type hinting

#415 zktuong closed 4 weeks ago
0
fix clone id key

#414 zktuong closed 1 month ago
1
Remove `nxviz` from external

#413 zktuong opened 1 month ago
0
allow network downsample to work on any locus

#412 zktuong closed 2 weeks ago
0
Remove python 3.9

#411 zktuong opened 1 month ago
1
"clone_id" not found

#410 zktuong closed 1 month ago
0
pip dev(deps-dev): update sphinx-autodoc-typehints requirement from <=2.2.3 to <=2.3.0

#409 dependabot[bot] closed 3 weeks ago
3
Fix anndata compat

#408 zktuong closed 1 month ago
1
ImportError with latest AnnData

#407 grst closed 1 month ago
1
pip dev(deps-dev): update sphinx-autodoc-typehints requirement from <=2.2.2 to <=2.2.3

#405 dependabot[bot] closed 2 months ago
0
assert sample names as strings during preprocessing

#404 zktuong closed 2 months ago
1
Add a return step to gently deal with preprocessing failures during the tigger step.

#403 zktuong closed 2 months ago
1
Clean up warnings

#402 zktuong closed 2 months ago
1
pip dev(deps-dev): update scirpy requirement from <=0.17.0 to <=0.17.2

#401 dependabot[bot] closed 2 months ago
1
Error when running ddl.pp.quantify_mutations()

#400 palak-genge closed 2 months ago
3
pip dev(deps-dev): update scirpy requirement from <=0.17.0 to <=0.17.1

#399 dependabot[bot] closed 2 months ago
1
ddl.to_scirpy throws an error: "Value passed for key 'airr' is of incorrect shape"

#398 Nithishwer closed 2 months ago
7
fix isotype parsing

#397 zktuong closed 3 months ago
2
error dandelion/utilities/_core.py KeyError: 'trbc*'.

#396 lishuangshuang0616 closed 3 months ago
3
pip dev(deps-dev): update sphinx-autodoc-typehints requirement from <=2.1.1 to <=2.2.2

#394 dependabot[bot] closed 3 months ago
1
Singularity Container Preprocessing Error from container

#393 m21camby closed 3 months ago
1
TypeError: clone_overlap() got an unexpected keyword argument 'colorby'

#392 NicolaasVanRenne opened 3 months ago
1
fix MakeDb_gentle.py file name

#391 zktuong closed 3 months ago
1
Igblastn error for Human and not Mouse

#390 Kfirinb closed 3 months ago
1
Singularity Error: raise ValueError(f"cannot insert {column}, already exists")

#389 bluenikolas closed 3 months ago
2
pip dev(deps-dev): update sphinx-autodoc-typehints requirement from <=2.1.0 to <=2.1.1

#388 dependabot[bot] closed 3 months ago
1
No such file or directory: 'MakeDb_gentle.py'

#387 hungms closed 3 months ago
3
adjust manual_threshold to skip running findThreshold

#386 zktuong closed 3 months ago
1
pip dev(deps-dev): update scirpy requirement from <=0.16.1 to <=0.17.0

#385 dependabot[bot] closed 4 months ago
0
fix matplotlib compatibility

#384 zktuong closed 4 months ago
2
Incompatibility with latest matplotlib

#383 grst closed 4 months ago
2
IGDATA vs. IGBLAST_DB Confusion + Other Installation kerfuffles

#382 indianewok opened 5 months ago
1
remove testing on macos-latest because there's no blast/igblast available

#380 zktuong closed 5 months ago
1