User: lshepard

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lshepard430
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Posts by lshepard

<prev • 84 results • page 1 of 9 • next >
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Comment: C: Should you normalise gene expression data before meta analysing?
... And to complement, before doing any intersample comparison, you could do some QC (e.g. PCA), after normalization but before any statistical comparisons. This would give you an idea if there any any other factors you should consider for your analysis. ...
written 8 weeks ago by lshepard430
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Comment: C: Transcript level counts from full length scRNA data
... ^ added a question for follow-up in the Bioconductor forum for those who are interested: https://support.bioconductor.org/p/132550/ ...
written 11 weeks ago by lshepard430
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Comment: C: Transcript level counts from full length scRNA data
... Thanks Michael. I will go ahead and post a topic there to continue this conversation. I think at this point it's clear the community could benefit from further discussions on this. ...
written 11 weeks ago by lshepard430
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Comment: C: Transcript level counts from full length scRNA data
... I don't think so... (could be wrong, open to feedback). I believe that providing the counts seems to be the route to take mainly based on: 1) the fact that counts returned `countsFromAbundance=lengthScaledTPM` are corrected for length bias in addition to depth/library size 2) In Seurat, there is an ...
written 11 weeks ago by lshepard430
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Comment: C: Transcript level counts from full length scRNA data
... How did you import the Salmon counts into Seurat? With Alevin, it's recommended that the counts be imported without length correction, but here since this is full-length I am assuming we would want some type of length correction as it is done with `tximport`. Perhaps still using `txi$counts` but wit ...
written 11 weeks ago by lshepard430
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Comment: C: Difference between annotation from Ensembl and UCSC.
... Indeed, but be aware that there are minor differences in chromosomal coordinates between Ensembl and UCSC (e.g.: if someone uses Ensembl genome + annotation, this will be 1bp off from UCSC genome + UCSC annotation. Importantly, when I mention UCSC annotation, this goes for all the annotation UCSC ho ...
written 10 months ago by lshepard430
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Comment: C: To generate an scRNA counts file using barcodes.tsv, genes.tsv and matrix.mtx fi
... No, Seurat does not require the data to be in csv. Use `Read10X` to import your 10X data for object creation. ...
written 13 months ago by lshepard430
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Comment: C: Promoter in gene body region of another gene - feedback on definition or consens
... Very true Kevin, thank you for that additional thought and thank you Devon. ...
written 15 months ago by lshepard430
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Comment: C: Promoter in gene body region of another gene - feedback on definition or consens
... Emily, thank you so much for this reply, and all the work from Ensembl. This helps me greatly. ...
written 15 months ago by lshepard430
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Promoter in gene body region of another gene - feedback on definition or consensus
... Hi everyone, I am wondering if there is a standard/consensus about how we ***should*** define promoter regions which may fall upon gene body regions of another gene. To expand: say I define a promoter as 1000 bp away from the TSS and I want to intersect CpG methylation to find regulatory regions (g ...
annotation written 15 months ago by lshepard430 • updated 15 months ago by Emily_Ensembl21k

Latest awards to lshepard

Great Question 9 months ago, created a question with more than 5,000 views. For Differential expression of scRNA-seq after Seurat
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Running STAR aligner with paired-end and single-end reads simultaneously
Scholar 15 months ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Popular Question 16 months ago, created a question with more than 1,000 views. For Rsubread installation issues
Scholar 16 months ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Popular Question 17 months ago, created a question with more than 1,000 views. For Rsubread installation issues
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: Running STAR aligner with paired-end and single-end reads simultaneously
Supporter 19 months ago, voted at least 25 times.
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Rsubread installation issues
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Rsubread installation issues
Scholar 2.8 years ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Scholar 2.8 years ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Scholar 3.2 years ago, created an answer that has been accepted. For A: which one is adapter and which one is index
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: which one is adapter and which one is index
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Rsubread installation issues

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