Chuang1118

Thank you very much for this explanation! Now, I do some post-check to see spatial pattering of the BCR has located the plasma zone using A_102_0023_FR2_barcode_airr.tsv for example. Even if...

Hello mourisl, option --fact is useful for me, I have used frac == 0 to get complete output. script barcoderep-expand.py and trust-airr.pl are work, except you've forgot to comment line...

@mourisl I observed no productive barcode doesn't have cdr3, maybe 279nt from FR2 is not enough sometimes, but I got constant region sometimes. I have other version from FR1, here...

I use TRUST4 by building singularity container and launch job by Snakemake, because I've also gene expression part. Now, I am in stage define parameters hardware in multiple cores server....

Hello Hana, Thank you for your suggestion, this make sense for me. Here, I have big celltypes. In my opinion, all the method can handle big celltypes, it cannot represent...

Hello Hana, I have a question about AutoGeneS*. I don't know how to add genes additional. After : ``` ag.optimize(ngen=5000,nfeatures=400,seed=0,mode='fixed') ``` Each pareto solution is a set 400 genes. Then...

same issue, Did you find a solution ?

Hello Author, For more informations, I upload the matrix called fim as your code in https://github.com/theislab/ncem/blob/1ed3ccead38f70fcdbcc6640971ddfa877ff62cd/ncem/utils/wald_test.py#L8 For building fim matrix, I am following previous Traceback messages. **Additional context** ``` (fim<...

Hi ArtRand, Please find attached. [mock_1_bigWig.log](https://github.com/user-attachments/files/21738658/mock_1_bigWig.log)

I have other pipeline using `modkit bedmethyl tobigwig` to get genomic coordinates bigwig instead of transcriptome bigwig 1/ conversion transcript coordinates to genomics 2/ sorting 3/ to bigwig I got...