User: jomo018

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jomo018610
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Posts by jomo018

<prev • 104 results • page 1 of 11 • next >
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Answer: A: "Idents" can not be use in seurat
... Try: Idents(D3_APLNR)=D3_APLNR$res.0.3 ...
written 12 days ago by jomo018610
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Comment: C: A list of human cell cycle genes for Seurat
... The list of Shicheng Guo seems to originate from [A high-resolution transcriptome map of cell cycle reveals novel connections between periodic genes and cancer][1] Table S2 (67 core genes). [1]: https://www.nature.com/articles/cr201684#MOESM19 ...
written 24 days ago by jomo018610
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Comment: C: type='apeglm' shrinkage only for use with 'coef'
... Is `dd1` one of the members of `resultsNames(dds)` as required ? ...
written 27 days ago by jomo018610
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Comment: C: Question: can not obtain DESeq2 results
... Check [https://support.bioconductor.org/p/127239/][1] [1]: https://support.bioconductor.org/p/127239/ ...
written 27 days ago by jomo018610
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Comment: C: Classic threshold for log2 fold change in RNA-seq experiment
... if you want Fold Change above 1.5 than you need to set the limit for log2FoldChange at log2(1.5), not 1.5. ...
written 4 weeks ago by jomo018610
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Comment: C: Deterimining overall number of differentially expressed genes between WT and KO
... @singcell - it is probably better to convert your response from ***answer*** to ***comment***. Otherwise, please provide more details about the problem that you actually see. ...
written 4 weeks ago by jomo018610
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Comment: C: Deterimining overall number of differentially expressed genes between WT and KO
... With `ident.1="KO"` and `ident.2="WT"`, positive `avg_logFC` from `FindMarkers` indicates **over-expression** of **KO** relative to **WT**. ...
written 4 weeks ago by jomo018610
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Answer: A: Deterimining overall number of differentially expressed genes between WT and KO
... You need to define `ident.1` in `FindMarkers` and cannot keep it as `NULL`. Allowed idents are members of the named vector `Idents(seurat_obj)`. The names of this vector are **cell names**. Originally, `Idents(seurat_obj)` holds **cluster indices** which lends itself to find markers between cluster ...
written 4 weeks ago by jomo018610
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Comment: C: Relative variance in PCA of scaled data of scRNA-Seq
... A quick glance at chapter 9.2 of [osca][1] sort of suggests sending us back to square one. if top PCs capture **coordinated biological processes** while the long tail of other PCs is mainly random noise, the denominator of `% explained` should probably be the sum of those top PCs. [1]: https:// ...
written 6 weeks ago by jomo018610
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Comment: C: Remove ensembl identifiers from Seurat
... I think this does not work with complex objects like a seurat object. ...
written 6 weeks ago by jomo018610

Latest awards to jomo018

Centurion 27 days ago, created 100 posts.
Student 7 weeks ago, asked a question with at least 3 up-votes. For De-duplicate UMI at FASTQ level
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to remove the empty line in using python
Popular Question 5 months ago, created a question with more than 1,000 views. For Pair end merging and statistical output
Scholar 9 months ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Popular Question 9 months ago, created a question with more than 1,000 views. For Pair end merging and statistical output
Popular Question 12 months ago, created a question with more than 1,000 views. For fastq reads with primers and truseq indexed adapter
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?
Popular Question 16 months ago, created a question with more than 1,000 views. For fastq reads with primers and truseq indexed adapter
Popular Question 18 months ago, created a question with more than 1,000 views. For fastq reads with primers and truseq indexed adapter
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Scholar 2.5 years ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?
Commentator 3.1 years ago, created a comment with at least 3 up-votes. For C: Why not merging?
Scholar 3.4 years ago, created an answer that has been accepted. For A: Illumina paired-end reads R1 and R2 mixed together?
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Illumina paired-end reads R1 and R2 mixed together?

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