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Dear Developers,
Thank you for your work. I tried TedSim and manage to simulate a dataset as explained in the vignette.
## Context
The default implementation of TedSim allows for simulation o…
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Dear Rongxin,
can I add additional metadata to 1) single barcodes/cells or 2)even only to whole experiments during "createSnap"?
Concerning 1 I want to add protein-expression values and then visu…
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Hi,
I am trying to run velocyto using run10x command. I'm running on cluster by requesting 60 GB memory. Do I need more memory for that? Thank you so much for your help.
initial position.
2019-0…
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Hello. I am currently trying to realign the raw data from this paper using the kallisto-bustools pipeline. I am able to specify custom technology by demarcating which read and the start and end positi…
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I used VarTrix to extract single cell variant information from our 10x Genomics single cell data
$vartrix --bam $out_bam --cell-barcodes $barcodes --fasta $fasta_file --vcf $out_vcf --out-variants $o…
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hello, I'm using cell2cell to identify interactions with scRNAseq data.
```
interactions = c2c.analysis.SingleCellInteractions(rnaseq_data=rnaseq,
…
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### Please confirm if bug report does NOT exist already ?
- [X] I confirm there is no existing issue for this
### Steps to reproduce ?
When clicking on the "+" of a lookup field in the table or gri…
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Dear BLAZE developers,
I was wondering if the BLAZE pipeline can be used with a different single-cell protocol than 10X.
If our single-cell protocol has a different Adapter sequence, and we have …
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Hi,
Thanks for developing a subset-bam software. I would like to split the BAM file (from cell ranger) for each individual cell barcode, which is provided in the filtered_feature matrix folder (bar…
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I would like to ask how Trust4 can directly analyze paired-end .fastq format data from the 10X Genomics platform for single-cell analysis, instead of analyzing BAM format data. Can you provide support…