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Hi, I just report problematic named entities I found using `en_core_sci_sm`, to improve the model. Most of them contain unbalanced brackets.
```
(-2)-0-(+2
(-8
(= control values
(= controls
(=…
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https://mp.weixin.qq.com/s/OxrJxDaLKQhxMzpuZkqn9A
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Hi,
I am currently working on SE analysis for a set of samples. For all samples, the analysis went well in the ROSE_callSuper step. However, in the ROSE_geneMapper step, I got *_SuperStitched_GENE_…
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Hello,
Thank you for the great tool.
One question I have after reading the paper, also looking the code, is seems that the peak-gene pairs are predicted using cells from one cell type (cluster)…
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Jie Liu (Cincinnati Children's) wrote on 9/23:
> I have been struggling for a while about gene fusion scope/definition/nomenclature issues.
>
> To have a standardized nomenclature for the fu…
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Hello, I'm trying to replicate your prediction results for "CD4-positive_helper_T_cell-ENCODE" published in [Nature at 2021](https://www.nature.com/articles/s41586-021-03446-x#Sec9): as shown in the […
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### Description of feature
Dear CREsted dev,
Thank you very much for this tool and the step by step tutorial. I managed to generate a model however, when I tested, the result was disappointing:
```…
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Hello everyone, great fan of this work! I have a question:
Is there any chance to get access to (already computed) a genome-wide scent peaks database? Does this dataset exist?
Bests,
Gabriel…
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Hello! Your software is really great, but I only have ATAC-Seq, Hi-C data, but no H3K27ac ChIP-Seq data. Can I use this ABC model for enhancer-gene prediction.
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Hi, I'm trying to use the public data as mentioned in the supplementary file: H3K27ac-ChIP: ENCFF384ZZM and DHS: wgEncodeUwDnaseK562AlnRep1.bam, wgEncodeUwDnaseK562AlnRep2.bam. And I also change the r…