Alan Murphy

Output bigwigs with macs2 p-value signal for every base-pair

4

I am looking for the MACS2 p-value signal for every base-pair, similar to the bigwigs available from [ROADMAP](https://egg2.wustl.edu/roadmap/data/byFileType/signal/consolidated/macs2signal/pval/) or [EPIMAP](https://epigenome.wustl.edu/epimap/data/observed/). Had a discussion with @JoseEspinosa and he thinks it may...

imperial_mb.config

1

Hey, Not sure if you are aware but the large med-bio queue (as used in the imperial_mb.config) has been deprecated but annoyingly you can still submit jobs to it and...

Use for pseudobulk differential expression - advantages & logFC values

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Hi, Thank you for your very useful package. I have two questions regarding its use for pseudobulk differential expression analysis. Firstly, could you outline the reasons why you think your...

Hi, Is there a pre-trained version of the model available for use to predict in new cell types? Cheers

Extend quality control and standardisation to QTL analysis

2

Extend quality control and standardisation to QTL analysis. Following checks are specific to QTL studies and need to be added: * Allow for duplicated SNPs * Check effect region/gene region...

Hi, I'm trying to replicate Chromoformer's self-attention map as analysed in [Fig. 4a of your publication](https://www.nature.com/articles/s41467-022-34152-5#Fig4). The description given in the results is: > the attention weights produced by the...