MAESTRO
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liulab-dfci
Single-cell Transcriptome and Regulome Analysis Pipeline
Hi, I am trying to use the RP model to generate the gene activity score to 10x scATAC data. I installed MAESTRO R version as well as python version and...
How to run the pipeline with Smartseq2 raw data? The current MAESTRO Website did not provide it.
Hello, thank you for developing MAESTRO! I am someone that is fairly new to ATAC-seq analysis. I am trying to use MAESTRO for 10X scATAC-seq using the latest version and...
Change type of `int8` to `int32` to avoid negative count values.
I noticed that unlike RNA analysis, the original identities aren't assigned to the Seurat object when using `ATACRunSeurat`. I propose to add the same behaviour where: - The `orig.ident` is...
Hi I'm interested in utilizing this pipeline. Does Maestro support rn6 Rattus norvegicus?? All the best Sincerely Jeff Jaureguy
The value range of gene_peak matrix in RP_model should between 0 and 1. Why does "genes_peaks_score_csr" in scATAC_Genescore.py have a value greater than 1, with a maximum of 1600+.
Based on the [MAESTRO paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02116-x#Sec12), my understanding is that a peak that is in the exons or promoter region of more than one gene is scored as 0 for all...
the genedistance parameter https://github.com/liulab-dfci/MAESTRO/blob/master/MAESTRO/Snakemake/scATAC/Snakefile#L1166 is not used in the shell command https://github.com/liulab-dfci/MAESTRO/blob/master/MAESTRO/Snakemake/scATAC/Snakefile#L1174 Using default 10,000 bp.
Is it possible to pass in an existing Seurat object (or converted SingleCellExperiment object)? I have a pretty robust pipeline that does QC, clustering and such, would like to have...
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Single-cell Transcriptome and Regulome Analysis Pipeline