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26 Open 32 Closed
26 Open 32 Closed
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Issues list

# Perform dimensionality reduction and clustering of GEX and TCR data. # UMAP reduction and louvain clustering are the defaults. adata = conga.preprocess.cluster_and_tsne_and_umap(adata) print('adata.shape:', adata.shape) print('adata.obs_keys():', adata.obs_keys()) print('adata.obsm_keys():', adata.obsm_keys())
#72 opened Sep 19, 2024 by szy23333
using CONGA on multiplexed data?
#69 opened May 11, 2024 by jjs847
deal with TRDV1_TRAJ_TRAC sequences
#68 opened Mar 24, 2024 by guillemsanchezsanchez1996
Only CDR3 Region?
#67 opened Mar 12, 2024 by TheRaspberryFox
1
Question about the _compute_graph_overlap_stats() function
#66 opened Feb 21, 2024 by xiachenrui
Question about --nbr_fracs
#64 opened Sep 25, 2023 by anchormok
5
Issue with logo plots
#62 opened May 30, 2023 by guillemsanchezsanchez1996
1
running Conga on integrated Seurat Gex
#61 opened May 19, 2023 by SamWell16
1
pMHC data processing
#60 opened Apr 13, 2023 by leeanapeters
1
Mouse BCR
#58 opened Jan 11, 2023 by DennisCambridge
5
What does spurious chain sharing mean?
#56 opened Nov 22, 2022 by chuckzzzz
10
Just make Logo plots starting from TCR data
#54 opened Nov 7, 2022 by erosix
5
ImportError: cannot import name 'PathLike'
#53 opened Oct 30, 2022 by zhao-xinlu
1
Error in Aggregate the individual GEX runs into a single AnnData object
#52 opened Oct 24, 2022 by QianhuiXu
2
run_conga.py error = UnicodeEncodeError: 'ascii' codec can't encode character '\xd7' in position 26: ordinal not in range(128)
#51 opened Sep 23, 2022 by shimbrianh
what is mean of ‘raw_count’ in tcr_clumping?
#50 opened Sep 1, 2022 by mabaoweireadingene
AssertionError in conga.plotting.make_graph_vs_graph_logos()
#49 opened Aug 26, 2022 by cr2106
1
Plot epitope specificity on GEX umap
#48 opened Aug 21, 2022 by cr2106
1
update mouse tcr gene reference
#45 opened Jun 30, 2022 by sschattgen
2
Where iMHC scores are stored in the data model?
#44 opened May 9, 2022 by markgene
2
make_tcr_clumping_plot failing when trying to save figure
#41 opened Mar 4, 2022 by AvivBenchorin
4
speed up graph-vs-feature analysis on large datasets
#37 opened Jan 18, 2022 by sschattgen
Compare multiple sample groups
#34 opened Dec 1, 2021 by cr2106
7
Question: plotting batch info when running vai run_conga.py script
#32 opened Nov 26, 2021 by s2hui
1
Question: Is it possible to run with BCR sequences
#25 opened Oct 1, 2021 by ghost
3
ProTip! What’s not been updated in a month: updated:<2024-09-01.