conga
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phbradley
Clonotype Neighbor Graph Analysis
Hello Phil, I have found in some of my sc 10x vdj data sequences that contain a TRDV1 gene segment combined with TRAJ and TRAC genes (see this recent paper...
Hello, I have very much enjoyed using your program. Currently, the TCR clusters are being formed exclusively around differences in TRAV gene usage. With no visible differences in CDR3 region...
Hi all, I found following code in `_compute_graph_overlap_stats()` function, but I can not understand it. How do you calculate the `f'log10_overlap_sdev`, `log10_expected_overlap` and `total_log10_indegree_variance`, and what do them mean? I...
Hi Philip! Thank you so much for this amazing tool! It has helped tremendously with fine T cell annotation in our mice sample. I saw that back in 2020 you...
Hi! Thanks for developing this amazing tool. I have a conceptual question regarding the filtering step. In the paper, you mentioned: > Here, by default, the 10x cellranger clonotype definitions...
Hi everyone, A wonderful package to link scRNA and scTCR!! Recently I test the run_conga.py script and found that CoNGA scores in TCR2D was easily influenced by argument 'nbr_fracs'. When...
Hello everybody, First of all thanks a lot Conga team for creating this nice and cool package, and for keeping in mind the gd TCR "aficionados" in your work. I...
I am trying to run Conga on my integrated Seurat object. I already downsampled and integrated 4 CITEseq data in a Seurat object. I have TCR csv file for each...
Hello, I have some groups of single cell TCRs for which I would like to make Logo plots including both alpha and beta chains and the usage of V and...
Hi, thank you for the great package! I have run this pipeline successfully without incorporating pMHC information but would like to add this in. I was wondering if you could...
