UCSCXenaTools

UCSCXenaTools copied to clipboard

Error in fetch_dense_values

2

Hello, thank you for the wonderful tool. First time posting, so please let me know if this issue has been solved elsewhere (I couldn't find) or if more information would...

jbagnot

UCSCXenaTools: Retrieve Gene Expression and Clinical Information from UCSC Xena for Survival Analysis

1

Hi, I tried to use the markdown published on https://ropensci.org/blog/2019/09/06/ucscxenatools-surv/ This is what happens: merged_data = tibble(sampleID = names(KRAS), KRAS_expression = as.numeric(KRAS)) %>% left_join(cli, by = "sampleID") %>% filter(sample_type ==...

gbregni

how to get log(TPM+1) values

4

Thank you for this tool. I am a novice in all TCGA data, but I am looking to do some analysis, and I wanted to download TPM normalised values, so...

sunta3iouxos

Enhancements

1

1. fetch_dataset_samples(host, dataset) failed in query all samples Don't know why ``` > fetch_dataset_samples(host, dataset) Error in FUN(X[[i]], ...) : is.atomic(p) | is.list(p) is not TRUE ``` Change to `fetch_dataset_samples(host,...

ShixiangWang

Retiring the old GDC data hub   Last year we updated the GDC data on Xena and on Friday December 5th,

1

ShixiangWang

including part of #42

ShixiangWang