User: jmah

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jmah10
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Posts by jmah

<prev • 39 results • page 1 of 4 • next >
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Comment: C: plotting trees in R: node labels from nexus tree files
... Thank you! I'll give that a try. Also, thanks for making ggtree! I love that package. ...
written 2 days ago by jmah10
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Comment: C: plotting trees in R: node labels from nexus tree files
... To clarify, the node labels I am after are the posterior probabilities ("posterior"). ...
written 6 days ago by jmah10
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plotting trees in R: node labels from nexus tree files
... Hi, I am trying to plot a phylogeny from RevBayes in R. The trees are in nexus format. For some reason, node labels do not import when I use ape::read.nexus(). When checking the phylo object, it shows that branch lengths have been imported, but no node labels. I am able to see the node labels in ...
ape ggtree nexus revbayes R written 6 days ago by jmah10 • updated 3 days ago by Guangchuang Yu2.4k
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stepwise time-dependent speciation decline vs diversity dependent decline without extinction
... I have a species phylogeny and am interested in studying diversification dynamics, I am using the (R package DDD][1] to assess whether density dependent vs time dependent diversification has occurred. In particular, I am using the function bd_ML() and I am trying to understand the description for th ...
speciation R diversification ddd extinction written 8 weeks ago by jmah10 • updated 18 days ago by Biostar ♦♦ 20
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Comment: C: Normalization across different single cell RNAseq experimetns
... Thanks! That's all very helpful. I appreciate your help! ...
written 5 months 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 5 months 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 5 months 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 5 months 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 5 months 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 5 months ago by jmah10

Latest awards to jmah

Popular Question 5 months ago, created a question with more than 1,000 views. For OrthoMCL step 12: [mclxReadDimensions] could not parse header
Popular Question 11 months ago, created a question with more than 1,000 views. For GO enrichment - interpreting broad terms
Popular Question 15 months ago, created a question with more than 1,000 views. For GO enrichment - interpreting broad terms
Popular Question 20 months ago, created a question with more than 1,000 views. For HMMER error: Unrecognized format with Pfam-A.hmm
Popular Question 20 months ago, created a question with more than 1,000 views. For GO enrichment - interpreting broad terms
Popular Question 3.3 years ago, created a question with more than 1,000 views. For HMMER error: Unrecognized format with Pfam-A.hmm
Scholar 3.5 years ago, created an answer that has been accepted. For A: HMMER error: Unrecognized format with Pfam-A.hmm

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