TAPE

TAPE copied to clipboard

reproducing result for pbmc

2

Thank you for sharing the script and the input pbmc_data.h5ad. I was able to reproduce the good performance with the script TAPE_realbulk.ipynb. However, when I extracted the input training and...

fanying2015

Data format for bulk RNA-seq with 10X UMI data as reference: counts, TPM or PFKM?

3

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...

Junjie-Hu

data normalization

2

Thanks for this wonderful tool. I have one question: when I simulated Psedobulk data using sc-RNAseq data, I just check the function "generate_simulated_data", it looks as print('Normalizing raw single cell...

doulijun777

TranscriptLength is easier to get comparing to transcript start and end

2

No need to calculate the gene len if the file already provided.

loganylchen

Popping Figure

1

Dear Sir or Madam, I am performing a benchmarking of deconvolution methods and I need to run TAPE and Scaden many times on multiple datasets. I wanted to know if...

alexdray86

ValueError: Found array with 0 sample(s) (shape=(0, 5000)) while a minimum of 1 is required by MinMaxScaler

2

Hello, I'm glad to learn this excellent paper. There is a problem with the running of this paper, which takes up your time. I hope to get your reply. After...

renruichen

Guidance on selecting parameters and choice of data scaling

1

Hi, I've been using TAPE to deconvolve some cases from the TCGA dataset using reference single-cell sequencing (from 100-200 cells per phenotype, from 6 different phenotypes). It works well, and...

dr-michael-haley

Accessing signature matrix when adaptive = False?

4

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...

fojackson8

About program operation

2

Hello, I'm glad to learn this excellent paper. There is a problem with the running of this paper, which takes up your time. I hope to get your reply. I...

solitudetuzi

Sampling takes too much time, can use GPU?

2

I am working with the GSE87544. It has 14k cells approx. The sampling is taking more than couple of hours. how to use GPU to accelerate this? I am unable...

abrarrahmanabir