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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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add synonyms to nifstd
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Probably a new pipeline entirely, and one that could follow directly after the current single_cell_RNAseq processing pipeline.
The primary goal will be separating outputs from the current pipeline pe…
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**tl;dr**: 3-tag sequencing methods for bulk RNA samples contain known sample indices and UMIs and thus resembles sc-RNA-seq read formats. Do you have a recommendation on how to use Salmon and / or Al…
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Hello, I am using music2_prop_t_statistics function to deconvolute ExpressionSet prepared wild type versus mutant bulk RNA-seq against an annotated SingleCellExperiment prepared scRNA-seq dataset that…
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Hi, I'm using the MarkerCount function to predict the cell type labels in my sc RNA-Seq data, but when I call the function like that:
df_res = MarkerCount( X=X, mkr_mat=marker_matrix, log_transform…
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**Describe the bug**
When I use code like following with npcs lower than 13 (like 12), it make error
```
adata_harmony=ov.single.batch_correction(adata,batch_key='batch',
…
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Hi,
After reading the tutorials carefully, I still feel confused how to prepare the input data. In most cases, users want to get cell-type fractions from tumor bulk RNA-seq data using the 10X data…
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Hola Ramon,
Vaig topar-me (per sort) amb el teu tweet on mostraves com fer uns plots molt macos combinant l'expressió de dos gens amb un objecte de single-cell rna seq.
Inspeccionant el teu code n…
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Hi,
I would like to use TRUP to detect chimeric fusions in my RNA-Seq datasets. Unfortunately, I keep running into the following issue:
# RTrace.pl --runlevel 4 --sampleName sample --seqType p --read…