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Hello,
I am using SpatialDecon to deconvolute bulk RNA seq data. I'm using log2-transformed and normalized counts for the norm matrix and creating a custom cell profile matrix. I originally tried usi…
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Hello!
I'm trying to run a bulk RNA-seq analysis using the following template:
```
# Template for human RNA-seq using Illumina prepared samples
---
details:
- analysis: RNA-seq
genome…
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If my bulk-RNA-seq data obtain from different time, does this matter?
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I found the paper "Multiplexed droplet single-cell rNA-sequencing using natural genetic variation" mentioned eight samples , but there are only five fastqs in EBI of SRP102802. and there are only…
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https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-5640/
@jburos found this dataset and described it as "containing RNAseq for TILs isolated from ccRCC samples"
We should take a look to see i…
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Thanks for your work! Excellent!
I have a question about the "Integration of expression data and binding matrices" section, related to figure 3A.
1. This should integrate multiple datasets, incl…
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Hello, thanks for providing such an amazing tools!
I noticed this tool is available for bulk RNA data. But since the scRNA-seq data is much more large and sparse, I don't know whether it can work w…
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I have a workflow question. Here is some background:
I have a Seurat RDS file of integrated ATAC-seq and RNA-seq data from human samples. This data measures TF expression. After running PCA and UMA…
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Predict how many samples you need for your next RNA seq experiment using available data for estimation of variance in genes for different tumortypes
User controls 1. gene, 2. tumorType, 3. isCellLi…
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Another form of sequence analysis is doing immune repertoire sequencing of the [VDJ recombination](https://en.wikipedia.org/wiki/V(D)J_recombination) locus in B and T cells.
For captured/enriched …