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When I use "CITE-seq-Count-R1./ SRR13724311_S1_L001_R1_001.fastq.gz-R2 SRR13724311_S1_L001_R2_001.fastq.gz-t Cmca9_tag_list_utf8.cfa-cbf 1-cbl 16-umif 17-umil 28 -cells 10000-o OUTFOLDER "is always no…
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I have a quick question about the snRNA-seq data of CCRCC samples that were used in this study. I downloaded the data from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE240822, following the d…
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Hello,
I'm getting the following error during UMI correction, when running CITE-seq-Count 1.4.5, Python 3.8.
```
Correcting umis
Traceback (most recent call last):
File "/data/home/hmy961/c…
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Dear team, thank you for your wonderful software RISC. It is great!
However, I run umap and find the clusters crowd together and overlap (pic in the attachment)
And the code below (scRNA is my Seura…
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Hi,
Is there an option in determineDropoutCandidates to handle missing value?
I made a reduced UMI count matrix for my single-cell RNA-Seq data. Then I had the "missing value" issue:
>x=read.…
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I see that the dropEst program reports a matrix of counts for genes in the input GTF. Would it be feasible to support output of a deduplicated BAM as well? I am not interested in scRNA-seq counts but …
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Hi Vivian,
I am trying to impute dropouts from a csv of UMI values ( 7 genes and 12244 cells).
The codes are listed below.
scimpute ("E:/gdT.csv", Kcluster = 2, out_dir = "E:/Cal", ncores = 1, dr…
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Hello,
first of all, thank you for this nice tool. We used it successfully on a time-series of bulk RNAseq samples, and it reflects nicely the maturation of our neuron cultures.
I was wondering now…
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Hi,
Thank you for developing such a wonderful tool!
I am currently looking to utilize the existing CNV profile via the `segs_consensus_fix `parameter to establish definitive CNV boundaries and stat…
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Hi,
I'm using the fast version of constructNull function, and the generated data have "NA" in it. The input matrix is a UMI count matrix, the command that I used is ` ClusterDE::constructNull(count…