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Hello,
I have been using your program to do imputation for some scATAC-seq data. I have a query regarding the output. The output for the both --binary and --impute function alter the peak annotation …
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Hi Authors,
Could you please provide the PBMC sample scRNA rds object and scATAC archR object used in the preprocessing_scRNA_scATAC.ipynb notebook?
It would be good to have with this so we can…
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> cat PUMATAC_tutorial-main/PUMATAC/src/singlecelltoolkit/processes/barcode_correction.nf
nextflow.enable.dsl=2
//binDir = !params.containsKey("test") ? "${workflow.projectDir}/src/singlecelltoolk…
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Hi,
I am using the MAESTRO to analyze a scATAC dataset downloaded form SRA database (accession number: SRR10399252), but I met this error:
```
Output file: Result/Mapping/SRR10399252_epilepsy/f…
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I have checked the format of the ATAC.se and the RNAmat.They are SummarizedExperiment and matrix. But when I ran runGenePeakcorr, I still have this problem.
```
cisCorr
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Hi,
I'm trying to install Taiji from the source code in our CentOS server using stack and I'm getting requested to give my github credentials during the installation:
```
[gascui@login02 Taij…
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I'm running a scATAC-seq analysis. The data was obtained from the published work: **Single-Cell Chromatin Accessibility Analysis Reveals the Epigenetic Basis and Signature Transcription Factors for th…
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I'm trying to run the `asap_to_kite_v2.py` script on scADT-seq data only. After running bcl2fastq, I only have read1 and read2, but see references to a read3 in the code that is causing me some errors…
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Thanks for your excellent software, thus making it possible for us to derive CNVs based on scATAC-seq data. After reading your code and introduction, I still have the following questions:
1 If I have…
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As we are refactoring scvi, I'm wondering what the utility would be to spin off the i/o part of scanpy into it's own lightweight package that's more general for reading single cell pipeline outputs in…