User: xiaoguang

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xiaoguang20
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Posts by xiaoguang

<prev • 13 results • page 1 of 2 • next >
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Can I use the SCENIC package to analyze the transcription factors in the bulk RNAseq data?
... The SCENIC package is software for the analysis of transcription factor activity and localized genes in single-cell transcriptome sequencing data, and the R package also scores the transcription factor activity of each cell. can I use the pack for bulk seq? ...
scenic rna-seq written 11 weeks ago by xiaoguang20 • updated 11 weeks ago by geek_y11k
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Comment: C: Open Source Mass Spec Search Engines?
... Is there any tutorial for X! Tandem software, I have n’t found it for a long time ...
written 12 weeks ago by xiaoguang20
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how to plot this picture?
... ![enter image description here][1] > This picture expresses the ligand and receptor interaction between cells. Color represents cell classification and gray represents gene expression. How can this graph be drawn? [1]: https://cdn.webchain.site/file/imgdisk-2/2020/03/09/hshs2019366946d27f67. ...
R circos written 3 months ago by xiaoguang20
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How to understand the multi-sample processing of Seurat?
... There is a question about `Seurat` that has been bothering me all the time. I would like to ask your opinions. For the case of multiple samples, In order to eliminate the batch effect, `Seurat` clustering will choose to integrate multiple samples, which is no problem. But when searching for markers, ...
rna-seq scrnaseq seurat written 4 months ago by xiaoguang20 • updated 3 months ago by Friederike5.7k
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Comment: C: When using monocle3 to calculate the pseudo time of 170,000 cells, an error is r
... Thank you very much! ...
written 5 months ago by xiaoguang20
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When using monocle3 to calculate the pseudo time of 170,000 cells, an error is reported, and the error is *** caught segfault *** address 0x2b3ae695f5c0, cause 'memory not mapped'
... When `monocle3` was used to calculate the pseudotime of 170,000 cells, `cds <-learn_graph(cds)`was run, but after calculating a few rounds, the error message was displayed as : ``` *** caught segfault *** address 0x2b3ae695f5c0, cause 'memory not mapped' Traceback: 1: .Call("R_euclidean_dist", ...
scrna written 5 months ago by xiaoguang20
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How to calculate pseudo time for all cells with monocle3
... I use the latest version of **monocle3** and follow the official tutorial to calculate the *pseudotime* ,but since there are two **partitions** in the calculation result, when I set the root node, half of my pseudotime is always gray. How can I do this for all Cell calculates pseudo time? my code i ...
monocle3 scrnaseq written 6 months ago by xiaoguang20
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How to get an exact match from the bam alignment file
... How to get an exact match from the bam comparison file, it is well known that M in the cigar character is completely consistent or there is mismatch, but how do I get a completely consistent sequence? ...
bam samtools bwa written 11 months ago by xiaoguang20 • updated 10 months ago by yasokannan9320
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Comment: C: how to caculate effective length for RNA sequencing?
... If we use featurecount, we can get gens quantification beacuse of aligning sequences to genome, but we use Salmon, we only get isoforms quantification. however,TPM is the percentage of FPKM,Are they different? ...
written 11 months ago by xiaoguang20
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how to caculate effective length for RNA sequencing?
... Is there any R packages or programs could help me to calculate **effective length** of every isoform or gene? We know the importance of effective length when we calculate TPM for isoforms or genes . but we can not got it from featurecount program. Salmon can get it ,but it is only for ...
R rna-seq written 11 months ago by xiaoguang20 • updated 10 months ago by Gordon Smyth1.7k

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