Yun YAN

Error: object 'seurat' not found when running 'exportFromSeurat' function

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**Demo** Here is a minimal reproducible example which uses the official Seurat's object and exports it to cerebro file via 'exportFromSeurat'. ```R library(Seurat) library(cerebroApp) cerebroApp::exportFromSeurat(object=pbmc_small, file='./crb.rds', organism='hg', column_cluster='res.0.8', column_sample='orig.ident', experiment_name='pbmc')...

I was wondering how can I collect and plot the accuracies results of all rounds after I successfully run the `SCCAF_optimize_all` function? I like the plot shown by the cli...

```R library(scales) set.seed(2020) c

**Problem** 1. Both the random colors and discrete color will not be repeatable in a new R session, as described in issue #13. 2. Setting seed as issue #3 did...

https://github.com/jianhong/ATACseqQC/blob/2996d20e9b39825b38d580b2c38636199975d29e/R/readBamFile.R#L47 The `interactive()` is anti-human and redundant. This is in particular annoying in Rstudio server. I highly suggest removing this condition.

## Motivation: Find the LR contributions that are **comparable** across pathways, sources, and targets. After using this PR, users can rank the LR from various pathways. Importantly, the contribution value...

UMAP is not available in report

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Hello, I found that the 'clustering' panel is blank in the report html file after I used the wrapper `process_no_dex`. All other things work out. I found the UMAP is...

Dedicated to the issue #22 . It works for `plot_hexbin_gene`. Top (before this PR) vs bottom (after this PR).

- [ ] if the parameters are properly set - [ ] if the input files are accessible: - [ ] GTF/GFF - [ ] command availability - [ ]...

practical suggestions to avoid an abrupt termination

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I came across some abrupt terminations when I used Cicero for the following two tasks: 1) creating the CCAN (chromatin hubs) and 2) inferring gene expression. Specifically, the function `generate_ccans`...