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Some attributes of the `Project` class were changed to a `@property`.
The user should be prohibited (raise error) or warned about this when trying to `setattr` on this type of attribute to prevent un…
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Relative to https://github.com/mc2-center/data-models/issues/49 and https://github.com/mc2-center/data-models/pull/66
Draft of the MC2 data model dictionary, using GitHub pages deployment, is here:…
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Hello,
I noticed there was code for evaluation in issue 29, but I want to ask the specific code used for calculating the insulation score, ''import insulation as insu''.
Additionally, I am intri…
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@thardy615
Please do a fresh pull and take a look at ```` prep/tannenbaum/geneTracks.R````
It won't run for you until you install the packages named at the top - but even before we/you sort th…
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Hello,
I am attempting to use MMARGE for analyzing ATAC-seq data from different strains of mice. I downloaded the SNP and Indel vcf files from the Mouse Genomes Project website and sorted them usin…
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Hi, it seems to me that we can only create a cistopic object using a matrix containing cell names as column names, regions as row names. If I already have a matrix, cell names as column and peaks as r…
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- Dataset: 941 features selected on 10X GE, then 10X GE -> AML PBMC_D11T1 gene score (original prediction by Seurat: Acc: 0.647 ARI: 0.409 MacroF1: 0.486, by MLP: Acc: 0.543 ARI: 0.169 MacroF1: 0.410)…
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## **Describe the bug**
I tried to run this pipeline multiple times, and it kept getting stalled at task=atac.read_genome_tsv:-1. But there's no error message. It only stopped when timeout.
f1ce-4…
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Hi,
I read your Nature publication (https://doi.org/10.1038/s41467-018-07771-0) and would love to generate aggregate single cell profiles in figure 3A and 4D's bottom panel for my data.
Could …
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**Describe the bug**
The DAG is incorrect for workflow github.com/hubmapconsortium/sc-atac-seq-pipeline/HuBMAP_scATAC-seq_Pipeline:feature/remove-curly-braces
after fixing https://github.com/dockstor…