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Hello!
I am running a differential contact analysis and I am now looking at the Chicdiff outputs. I am struggling to understand what each column represents for both the _results.rds and the getCand…
Mavti updated
2 years ago
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I could not find any detail about the "great apes classification task". This is not the same species classification task used in the HyenaDNA paper and so I am curious as to the number of species you …
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does not need involved in chromatin silencing?
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Similar to Issue #59 , expanding the other samplers to include support for regression models and other continuous-value-predicting models would allow users to analyze gene expression data, chromatin …
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### Lung-specific gene expression
- Identify the expression pattern for the marker genes of tissue-resident T cells
- [ ] integrate chromatin profiles with expression to validate the utility of …
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Real data sources to use:
1. Mutations from the [AWS S3 MultiAssayExperiment for ACC](https://github.com/waldronlab/MultiAssayExperiment/blob/master/inst/extdata/miniACC.R)
2. ABSOLUTE copy number c…
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Hello,
Thanks for developing this good tool to call chromatin loops. Our HiC sample just has ~150million valid pairs, do you think mustache can be used to call loops? and what resolution should …
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Add a function for RPKM, FPKM, and TPKM-like normalization, given total counts. For example, to normalize read counts/depth from chromatin accessibility assays.
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Dear developers,
I found that there needs a PWM format text as input in the config file. However, Jaspar only provides PFM text and the R library construct a PWMatrixlist how to get the PWM format …
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## Figure files
https://drive.google.com/drive/u/0/folders/1OLHVURBuAcLWaaI23athJjt3008-FHPE
## Panel legends
## Supplementary files
## Methods
## Reproducibility
### Code to gene…