User: jmah

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jmah10
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Posts by jmah

<prev • 35 results • page 1 of 4 • next >
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Comment: C: Normalization across different single cell RNAseq experimetns
... Thanks! That's all very helpful. I appreciate your help! ...
written 9 weeks ago by jmah10
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Comment: C: Normalization across different single cell RNAseq experimetns
... Of course, there would be a hierarchy of variation: variation between studies , and variation within studies that are due to the within-study batch effects. Thanks for pointing me towards Seurat and integration. So far it's the closest to what I'm looking for. Do you know of any methods that allow ...
written 9 weeks ago by jmah10
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Comment: C: Normalization across different single cell RNAseq experimetns
... Sorry, I must not be explaining this clearly enough. Each study is a big batch - we target the variation between different studies as if it were variation between batches. ...
written 9 weeks ago by jmah10
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Comment: C: Normalization across different single cell RNAseq experimetns
... I get that, but is it feasible to treat each different RNAseq experiment as if it were a batch in one big experiment, assuming I choose only studies that use the same sequencing and library prep method? ...
written 9 weeks ago by jmah10
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Comment: C: Normalization across different single cell RNAseq experimetns
... Thanks for pointing me towards some stuff. What do you think of the idea of only selecting studies that used the same methods (library prep, chemistry, machine etc). In other words, would that be as if analyzing one big study? Of course, there would still be much more variation between batches, beca ...
written 9 weeks ago by jmah10
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Normalization across different single cell RNAseq experimetns
... I'm interested in comparing single cell RNAseq experiments. RNAseq experiments are often normalized by some kind of global scaling scheme - each cell transcriptome is normalized by some scalar that has been calculated based on various factors - endogenous mRNA levels, capture + RT efficiency, diluti ...
single cell rnaseq batch effects global scaling written 9 weeks ago by jmah10
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Comment: C: Does Chromvar require bulk ATAC-seq?
... Thank you! That makes a lot of sense. I'm very new to this (if that wasn't obvious) and I really appreciate your help. ...
written 8 months ago by jmah10
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Comment: C: Does Chromvar require bulk ATAC-seq?
... erased and rephrased original q ...
written 8 months ago by jmah10
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Does Chromvar require bulk ATAC-seq?
... According to the Chromvar vignette (https://bioconductor.org/packages/release/bioc/vignettes/chromVAR/inst/doc/Introduction.html), "If analyzing single cell data, it can make sense to use peaks derived from bulk ATAC-seq". The wording is confusing. Do they mean use annotation of peaks defined by bul ...
chromvar scatac-seq atac-seq written 8 months ago by jmah10
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Comment: C: Chromvar for single cell ATAC seq
... That's a really thoughtful response. I didn't think of the consequences of assuming that clustering in one space may not correspond to clustering in another. In fact, I would need to check that by clustering by RNAseq and motifs, and seeing if those clusters overlap. Thanks for your help! You've gi ...
written 8 months ago by jmah10

Latest awards to jmah

Popular Question 7 months ago, created a question with more than 1,000 views. For GO enrichment - interpreting broad terms
Popular Question 11 months ago, created a question with more than 1,000 views. For GO enrichment - interpreting broad terms
Popular Question 16 months ago, created a question with more than 1,000 views. For HMMER error: Unrecognized format with Pfam-A.hmm
Popular Question 16 months ago, created a question with more than 1,000 views. For GO enrichment - interpreting broad terms
Popular Question 3.0 years ago, created a question with more than 1,000 views. For HMMER error: Unrecognized format with Pfam-A.hmm
Scholar 3.2 years ago, created an answer that has been accepted. For A: HMMER error: Unrecognized format with Pfam-A.hmm

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