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Hi `chromap` team,
Thank you so much for preparing this helpful tools and I'm very impressed by its performances. I am testing it on my scATAC-seq data and it works pretty good when I don't use `--…
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2 emails from Juliane
proposal
dccvalidator: https://cloud.r-project.org/web/packages/dccvalidator/vignettes/using-the-dccvalidator-pec.html
synapse: https://www.synapse.org/#!Profile:3432336/profi…
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**Describe the bug**
I succeeded to run `create_cistopic_object_from_fragments` and save the resulting `cistopic_obj` to dist. However, when I tried to run `run_cgs_models`, I got an error message as…
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Hello,
The fragment file returned by `chromap` is very useful for scATAC-seq, but sometimes, we need the peak by cell count matrix (or .mtx) for further analysis. Is there a way of getting this mat…
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Hi, I was working on mice E16 scATAC seq data. the raw data were downloaded from encode project, the motif data was downloaded from jaspar in a text file.
```
python
>>> import os
>>> os.getcwd…
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Hello,
I have 2 pooled snATAC donors and their individual bulk RNA-seq data. To demultiplex, my strategy was to call common variant SNPs for the two individuals separately using CellSNP, followed b…
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Hi, thank you very much for developing such a helpful tool! I am interested in mapping multimodal data such as SHARE-seq to reveal spatial patterns of chromatin accessibility, but I don't know how to …
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sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-…
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Hi， I'm runing the eNet for my own data, but the GPTab is NULL and without any error message:
Bellow is my code:
```
cre.mat
jphe updated
11 months ago