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During meetings on Mar 12 and 13, we (Matt, Becca, Rayna) decided we wanted to make the following four figures to address the research questions outlined in the [README.md](https://github.com/macmanes…
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Hi Vadim,
I just wondered about the following command description in your docs, which I suspect can possibly be misleading:
_**--relaxed-prot-inf** instructs DIA-NN to use a very heuristical pro…
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Dear EPEE team,
First of all, thank you so much for the great tool, EPEE.
I recently run EPEE tool on my gene expression data from RNA-Seq (2conditions/3 replicates each) and using an appropria…
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Hi,
I want to making a signature matrix using isolated cells, where the isolated cells have been sequenced using the bulk approach instead of the single-cell approach.
I am going to use sample 1-…
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My overarching goal is to pull down gene expression information for a known (set of) gene identifier(s) and contrast(s).
I currently use two endpoints to do this:
1. Dataset samples (https://gemma…
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Hi,
We have tried using Q3 and TMM normalisation for DSP WTA data. But when it comes to TCR spike-in add-on data, which normalisation methods (Q3, TMM or Poisson threshold model based normalisati…
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Dear music developers,
I got deconvoluted output from MuSic R library. I am interested in performing differential gene expression of the deconvoluted result.
I have following outputs upon deco…
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Dear,
I need to convert MSTRG.number into Gene name or Gene Symbol to be able to run on an R script that allows me to perform differential gene expression analyzes. From what I have been able to un…
ghost updated
3 years ago
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Hi,
I have read a paper called "Transcriptional diversity during lineage commitment of human blood progenitors" recently. In the paper, author used mmdiff to find cell-specificed genes and transcrip…
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Hello,
1. What is the smallest number of cells one can include in order to build an HSMM on in monocle?
2. What is the smallest number of genes one can use in monocle? In order to create HSMM object…