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Hi Margherita,
Thanks for your great work and sharing the data and code.I am using your mouse embryos spatial-ATAC data in mu project. While I have some problems in adding the image files and pos…
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https://mp.weixin.qq.com/s/9TUlAATcFbG3p2u33ZRtXw
ixxmu updated
11 months ago
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Hi @panushri25,
I am trying to also re-implement the bpnet model but for something similar to ATAC-seq (MOA-seq). It also captures "all" binding activity on the chromosomes (so not specific like Ch…
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We currently have 2 Collections that contain data from "10x multiome", an assay which measure both expression (RNA) & chromatin accessibility (ATAC).
- https://cellxgene.cziscience.com/collections/…
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**Primary Wrangler:**
Wei Kheng Teh
**Secondary Wrangler:**
Ida
**Associated files:**
Link to paper: https://www.biorxiv.org/content/10.1101/2022.01.11.474933v1.full
Google Drive: https://drive.g…
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Nice tool, congratulations! I would like to use it on 10x ATAC/multiome data. Could you please explain the following?
1. It would be great to see an example of how to start from `fragment.tsv.gz` s…
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Log File:
[ArchR-addGeneIntegrationMatrix-dcc6b48f59a-Date-2023-05-31_Time-04-15-42.log](https://github.com/GreenleafLab/ArchR/files/11608646/ArchR-addGeneIntegrationMatrix-dcc6b48f59a-Date-2023-05-3…
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We are interested in comparing Footprint Scores for individual binding sites across multiple (>2) conditions.
Based on your responses to some previous issues such as #19 and #87 it appears the foot…
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Hi,
I have run HINT v0.13.0 on bulk ATAC-seq data (skipping chrY and chrM) using command "rgt-hint footprinting --atac-seq --paired-end --organism hg19 --output-prefix "$p"_fp "$p".sorted.bam "$p"_…
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I installed ATACgraph according to instructions, and attempted to run the demo. Not sure if it's user error, but the first command, 00_rmChr doesn't work for me:
`$ ATACgraph 00_rmChr -h`
```
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