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excuse me ,I am facing an issue when running CIBERSORT package:
when I try this:
```
library(CIBERSORT)
sig_matrix
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Hello, I'd like to ask why, during experimentation with BCSS, it was observed that one class of predictions appears as black, although in reality the original labels were not black.
![TCGA-OL-A97C-DX…
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One approach is to process the raw data into summary statistics of interest. For instance, define a list of disease types and pool all the studies for that particular disease. Then calculate the mutat…
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**Describe the issue**
Hi I am planning to analyze copy number alterations in a small cohort (n=15), and I have the segmentation data in TCGA format. I tried to generate GISTIC files for maftools, ho…
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Hi,
Could you upload a patch example with its slide name,x and y position for each magnitude? I m trying to replicate your numbers with even a threshold of 30 but I still obtain 30000 patches at 20x.…
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### Description
in the following table definition, the comma of 3 lines:
is_ffpe text NULL -- is_ffpe; Indicator to signify whether or not the tissue sample was fixed in formalin and embedded i…
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Hi, I really enjoy your package.
I downloaded TCGA RNAseq fpkm value and try to produce the IPS as follows
`FPKMtoTPM
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Thank you for making this super useful software.
1. When running "compare_junctions_hist_v2.R", there were multiple NA values in "mean_norm_score_variant". I traced it back to the function starting o…
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Dear EcoTyper team,
Hi, all! Hope you been well and thanks so much for sharing amazing tool.
I was following tutorials using new TCGA data with in-house scRNA-seq dataset.
Initially, I run Tuto…
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Hi, I am getting the following error when trying to run histoqc on .svs files.
Command:
`python -m histoqc -c v2.1 -n 3 "./input_svs_test/*.svs"`
Error:
`
2024-07-03 15:43:52,680 - INFO - --…