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I de-convoluted 12 bulk RNA seq samples of brains from mice subjected to stroke. Each brain was separated into two hemispheres (Ipsilateral where ischemia took place and we expect neuronal death and …
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I open this issue to keep track of new methods and whether they should/should not be added to the package
- [Digitaldlsorter]( https://doi.org/10.3389/fgene.2019.00978): Deep learning based method…
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Hi Nanostring Team,
our working group is currently looking into this package of yours. We are trying to reproduce figures from the nature paper "Advances in mixed cell deconvolution enable quantifi…
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It seems that there's a problem with the "max_iter" returning a floating value 10000.0 instead of an int value as expected in the LogisticRegression. Does anyone know how to solve this problem? Thanks…
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- [x] Introduction - scope 0.5-1 page
- look into reviews
- broad overview into the field
- mention nature methods "method of the year 2020"
- define axis: targeted/high-resolution vs unbiased…
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Hi,
I'm interested in studying T cells specifically. So, I'd like to use the tool BayesPrism to quantify the various types of T cells within the bulk data, including CD8 T cells, CD4 T cells, NK T ce…
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Hello,
Firstly, thanks a lot for your tool, So far I've found your vignette really intuitive and your package really easy to use.
I'm currently testing how well deconvolution works on 'ground-…
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Hi there,
I have used BayesPrism to deconvolute my datasets utilizing reference data from a public database. My datasets consist entirely of human bone marrow mesenchymal stem cells and are not cance…
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Hello!
I am working through the tutorial and I have my own RNA-seq data that I would like to process with linseed. Does the LinseedObject function require data be formatted exactly as "GSE19830_ser…
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Hi,
I've been using TAPE to deconvolve some cases from the TCGA dataset using reference single-cell sequencing (from 100-200 cells per phenotype, from 6 different phenotypes). It works well, and is…