Skip to content

Issues: phbradley/conga

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

26 Open 32 Closed
26 Open 32 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

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! Type g p on any issue or pull request to go back to the pull request listing page.