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Hi,
I tried to run TRUST4 on paired end Bulk RNA-Seq Fastq files, but it failed with "139 at ./run-trust4 line 54" as shown in the screenshot below. Could you tell me what this error message means a…
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when i use the rawcount of RNA-seq data, the result is bad. Should i use log10(count+1) or log2(count+1) or TPM or FPKM? Which one is better? Thank you!
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Hi
I am using raw count data from single cell RNA-seq and bulk RNA-seq.
I am currently stuck at running the deconvolution function solveDampenedWLS().
I get the error :
```
Error in solve…
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If my bulk-RNA-seq data obtain from different time, does this matter?
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https://doi.org/10.1101/199315
>Single cell RNA sequencing (scRNA-seq) is a powerful technique to analyze the transcriptomic heterogeneities in single cell level. It is an important step for studyi…
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I wonder why avg_LFC column is multiplyed by "-1" in libra pseudobulk RNA seq output file.
I think It changed the direction of expression in DEG genes.
For example ,I ran the pseudo bulk RNA seq …
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Two Pulsar bugs:
1) In the scRNA menu, search for tissue (for instance lung) —> Search results are all bulk ATAC
2) Example: https://pulsar-encode.herokuapp.com/libraries/11405 this is a RNA …
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Hello. How can we provide/calculate "gene_length" and "reference_gep" for our bulk RNA-seq counts data? It is not clear from the paper and vignette how it was derived/created. Thank you.
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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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Hi, thanks for the nice paper and code.
As I understand it, the decoder function reconstructs the bulk RNA-seq input B from X (the predicted cell fractions). The learnt weights of the decoder func…