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Hi I am wondering if there is any documentation for 10x scATAC data?
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Hi,
I would like to reproduce the analyses you have done. In particular, using windows and harmony and or liger. But it is unclear for me (I apologize if I miss the information) How do you manage …
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Hi all,
cisTopic is a novel tool for single cell ATAC data analyzing, which applies the latent Dirichlet allocation (LDA) algorithm to reduce dimensions. It was reported that cisTopic can spec…
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Hello, I am learning scATAC-seq analysis recently. Thanks to signac package for the great help and good vignettes. But there is a confusing probelm when build ATAC Object. The matrix built from the fi…
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https://mp.weixin.qq.com/s/-ol394h5QaruwuJzhGVjQA
ixxmu updated
2 years ago
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The following issue was noticed when running `step2*.sh` from the tutorial.
Messages from `src/helpers/preprocessing/bam_to_bigwig.sh` are not being printed as expected.
The variables are not bein…
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## _Single-cell ATAC-seq data are sparse and noisy_
Article on scATACSeq methods: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02075-3
Existing template (ATACSeq): https://w…
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https://mp.weixin.qq.com/s/FlX3IY7b2rdk1_gSfo7eMg
ixxmu updated
2 years ago
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Obviously need data to test on. Getting both sharp (TF) and broad data (histone marks) and the various assays.
And preferably finding a region with decent peaks across these marks/assays (GAPDH, MY…
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Hi,
I followed the Signac tutorial to merge and integrate 5 scATAC objects.
To merge, I used https://satijalab.org/signac/articles/merging.html and
I saw some batch effect. So I went ahead …