phbradley conga issues - Githubissues

phbradley / conga

Clonotype Neighbor Graph Analysis

MIT License

83 stars 19 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

# 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 szy23333 opened 2 months ago
0
Where is the ‘Notes’ in ipynb?

#71 winglet0996 closed 4 months ago
1
Question re: GEX cluster assignments

#70 yls2g13 closed 6 months ago
3
using CONGA on multiplexed data?

#69 jjs847 opened 6 months ago
0
deal with TRDV1_TRAJ_TRAC sequences

#68 guillemsanchezsanchez1996 opened 8 months ago
0
Only CDR3 Region?

#67 TheRaspberryFox opened 8 months ago
1
Question about the `_compute_graph_overlap_stats()` function

#66 xiachenrui opened 9 months ago
0
Update fixup_gene_name() to select the lowest expect allele, rather than just *01 when no allele provided.

#65 bbimber closed 10 months ago
5
Question about --nbr_fracs

#64 anchormok opened 1 year ago
5
Support environment variable for preferred SVG to PNG utility

#63 bbimber closed 1 year ago
4
Issue with logo plots

#62 guillemsanchezsanchez1996 opened 1 year ago
1
running Conga on integrated Seurat Gex

#61 SamWell16 opened 1 year ago
1
pMHC data processing

#60 leeanapeters opened 1 year ago
1
make dev

#59 sschattgen closed 1 year ago
0
Mouse BCR

#58 DennisCambridge opened 1 year ago
5
calc_nbrs reworked for greater flexibility

#57 sschattgen closed 1 year ago
1
What does spurious chain sharing mean?

#56 chuckzzzz opened 2 years ago
10
what is mean of num_cells_w_tcr: 19055

#55 mabaoweireadingene closed 1 year ago
1
Just make Logo plots starting from TCR data

#54 erosix opened 2 years ago
5
ImportError: cannot import name 'PathLike'

#53 zhao-xinlu opened 2 years ago
1
Error in Aggregate the individual GEX runs into a single AnnData object

#52 QianhuiXu opened 2 years ago
2
run_conga.py error = UnicodeEncodeError: 'ascii' codec can't encode character '\xd7' in position 26: ordinal not in range(128)

#51 shimbrianh opened 2 years ago
0
what is mean of ‘raw_count’ in tcr_clumping?

#50 mabaoweireadingene opened 2 years ago
0
AssertionError in conga.plotting.make_graph_vs_graph_logos()

#49 cr2106 opened 2 years ago
1
Plot epitope specificity on GEX umap

#48 cr2106 opened 2 years ago
1
Empty clones_file

#47 kkearns13 closed 2 years ago
9
Merging Multiple TCR Files

#46 kkearns13 closed 2 years ago
3
update mouse tcr gene reference

#45 sschattgen opened 2 years ago
2
Where iMHC scores are stored in the data model?

#44 markgene opened 2 years ago
2
Error writing adata to file

#43 kjkrishnan closed 2 years ago
5
Merging with Batch Keys

#42 SandwichFiend closed 2 years ago
1
make_tcr_clumping_plot failing when trying to save figure

#41 AvivBenchorin opened 2 years ago
4
merge_samples errors

#40 AlicePsyche closed 2 years ago
6
subfigures (axes, gene symbols, features) cut off

#39 ViHammer closed 2 years ago
2
Writing out all_nbrs dictionary for reruns.

#38 sschattgen closed 2 years ago
1
speed up graph-vs-feature analysis on large datasets

#37 sschattgen opened 2 years ago
0
Save plots as svg

#36 cr2106 closed 2 years ago
1
TCR/BCR logos misaligned

#35 JingwenD closed 2 years ago
6
Compare multiple sample groups

#34 cr2106 opened 3 years ago
7
failed in merge_samples.py

#33 JingwenD closed 3 years ago
7
Question: plotting batch info when running vai run_conga.py script

#32 s2hui opened 3 years ago
1
weird GEX and TCR UMAPs

#31 coro1c closed 3 years ago
11
Question: num cells

#30 s2hui closed 3 years ago
5
conga.tcrdist.make_10x_clones_file.make_10x_clones_file

#29 afilaliM781 closed 2 years ago
1
Question about using previously integrated gex data

#28 s2hui closed 3 years ago
7
Just iMHC Scoring Method

#27 kanefos closed 3 years ago
2
Question: barcodes for cells

#26 s2hui closed 3 years ago
4
Question: Is it possible to run with BCR sequences

#25 ghost opened 3 years ago
3
AttributeError: Can only use .str accessor with string values!

#24 s2hui closed 3 years ago
2
KeyError: 'graph_vs_graph_logos'

#23 chris-rands closed 3 years ago
7