cell deconvolution tool Kassandra
Hi everybody,
I tried to use Kassandra, a deconvolution algorithm that estimates the proportion of cells in the Tumor microenvironment (TME). My RNA seq data is in a matrix format, where genes are in the rows, and samples are in the column. Values are TPM, also the FPKM on the other dataset. I trained the model as they said in the Tutorial LINK
I am not 100% sure if I understand their requirement and I’m wondering if Kassandra would work with datasets where the alignment was performed using tools such as STAR, Bowtie2, etc, other than Kallisto. If so, could you explain why that is the case?
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Confidence in CIBERSORT (LM22) Deconvolution Output for Rare Cell Types — Best Practices?
written by Pumla •
-
Trouble with CIBERSORTx: All P-values > 0.05, Low Correlation, High RMSE – What Could Be Going Wron…
written by Pumla •
-
Blog: Novogene Single-cell and Spatial Multi-omics Case Study II: Pan-cancer Research and Applicati…
written by Novogene •
-
If TPM is not comparable across cohorts, can it be used as the input for ML models if we have RNASe…
written by ivicts •
-
Seeking Guidance on Standardization Methods for eQTL Analyses with Diverse Preprocessing Techniques
written by DS •
-
Few lymphocytes detected by cell type deconvolution tools in lung adenocarcinoma
written by 350769816 •
-
Convert FPKM to TPM in R
written by AlexStar •
-
How to get transcript level estimates in TPM from TCGA BRCA
written by StartR •
-
Trouble with choosing the right reference transcriptome file for mm10
written by wyoo083 •
-
RNA-seq data analysis to detect dosage effect or proportional increase/decrease in expression acros…
written by nancy
kallisto is one of many valid ways to get a count matrix, so I doubt that is the only valid way. They just like that tool, so they seem to use it. bowtie2 is not splice-aware so it is not valid here.