hammerlab / multi-omic-urothelial-anti-pdl1

Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysis

Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysis

Numbers and Figures Linked to Source Analyses

In the interest of full transparency, please note that calculated numbers and figures are directly linked to their source Jupyter notebooks in this repository throughout our preprint.

Running the Code

To get started, install the requirements:

pip install -r requirements.txt

Create an ENV.sh modeled after ENV_TEMPLATE.sh, pointing to the data that you have available, and then call run.sh to source your ENV.sh in the context of a new Jupyter notebook.

rpy2

Certain notebooks in this repo require rpy2. rpy2 will be installed via the requirements.txt, but depending on your environment may require additional setup.

In order to execute the notebooks, you will need to have:

1. a functioning R install, preferably of a recent version of R.
2. certain R libraries commonly used.

Specifically:

# install R, if you haven't already
sudo apt-get install r-base r-base-dev

# create & set personal rlib directory, if not already done
# easiest way to do this is to open an interactive R console, and run 
> options(repos = 'https://cran.rstudio.com')
> install.packages('ggplot2')

## install certain R packages
R -e "options(repos = 'https://cran.rstudio.com'); install.packages(c('dplyr','survival','tidyr','ggplot2'));"

multi-omic-urothelial-anti-pdl1's Issues

TCR data

Hi,

Thanks for putting up all your analyses and data, it's a great resource!
I can't find the TCR CDR3 sequences anywhere though. Are you planning on releasing them?

question about your data

Is your file,“multi-omic-urothelial-anti-pdl1/analyses/bladder-kallisto-tximport.csv” representative gene expression matrix on each sample ? And is it processed by RNA-seq?

Error when using results() in the script bladder-deseq.R

Hi,

I'm using the bladder-deseq.R script and I'm stuck in this step:

deseq_results = results(dds, contrast=c("is_benefit", "True", "False"))

because it reports this error:

Error in if (!expanded & (hasIntercept | noInterceptPullCoef)) { : 
  argument is of length zero

Any ideas on how can I solve it?

Session info:

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 18362)

Matrix products: default

locale:
[1] LC_COLLATE=Spanish_Spain.1252  LC_CTYPE=Spanish_Spain.1252    LC_MONETARY=Spanish_Spain.1252 LC_NUMERIC=C                  
[5] LC_TIME=Spanish_Spain.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] gageData_2.24.0             gage_2.36.0                 DESeq2_1.26.0               readr_1.3.1                
 [5] tximport_1.14.0             SummarizedExperiment_1.16.1 DelayedArray_0.12.2         BiocParallel_1.20.1        
 [9] matrixStats_0.55.0          Biobase_2.46.0              GenomicRanges_1.38.0        GenomeInfoDb_1.22.0        
[13] IRanges_2.20.2              S4Vectors_0.24.3            BiocGenerics_0.32.0        

loaded via a namespace (and not attached):
 [1] bitops_1.0-6           bit64_0.9-7            RColorBrewer_1.1-2     httr_1.4.1             tools_3.6.1           
 [6] backports_1.1.5        R6_2.4.1               rpart_4.1-15           Hmisc_4.3-0            DBI_1.1.0             
[11] lazyeval_0.2.2         colorspace_1.4-1       nnet_7.3-12            tidyselect_0.2.5       gridExtra_2.3         
[16] bit_1.1-15.1           compiler_3.6.1         graph_1.64.0           cli_2.0.1              htmlTable_1.13.3      
[21] scales_1.1.0           checkmate_1.9.4        genefilter_1.68.0      stringr_1.4.0          digest_0.6.23         
[26] foreign_0.8-71         XVector_0.26.0         base64enc_0.1-3        jpeg_0.1-8.1           pkgconfig_2.0.3       
[31] htmltools_0.4.0        htmlwidgets_1.5.1      rlang_0.4.4            rstudioapi_0.11        RSQLite_2.2.0         
[36] acepack_1.4.1          dplyr_0.8.4            RCurl_1.98-1.1         magrittr_1.5           GenomeInfoDbData_1.2.2
[41] Formula_1.2-3          Matrix_1.2-17          Rcpp_1.0.3             munsell_0.5.0          fansi_0.4.1           
[46] lifecycle_0.1.0        stringi_1.4.5          zlibbioc_1.32.0        grid_3.6.1             blob_1.2.1            
[51] crayon_1.3.4           lattice_0.20-38        Biostrings_2.54.0      splines_3.6.1          annotate_1.64.0       
[56] hms_0.5.3              KEGGREST_1.26.1        locfit_1.5-9.1         zeallot_0.1.0          knitr_1.28            
[61] pillar_1.4.3           geneplotter_1.64.0     XML_3.99-0.3           glue_1.3.1             latticeExtra_0.6-29   
[66] data.table_1.12.8      png_0.1-7              vctrs_0.2.1            gtable_0.3.0           purrr_0.3.3           
[71] assertthat_0.2.1       ggplot2_3.2.1          xfun_0.12              xtable_1.8-4           survival_3.1-8        
[76] tibble_2.1.3           AnnotationDbi_1.48.0   memoise_1.1.0          cluster_2.1.0         
> 

RNA seq raw data

Hello
Could you inform me if the raw RNA seq data used in this analysis are publicly available for download somewhere?
Thanks,
Guillaume

Was the RNA-seq data here included in IMvigor210CoreBiologies R package?

@tavinathanson
Hi there,

I noticed that the data in this article and the data from the work of Mariathasan et al. both come from the IMvigor210 trial. However, the naming conventions for the patients in the two datasets are different, which makes it difficult for me to determine if they are the same. I was wondering if the RNA-seq data provided in this article is included in the IMvigor210CoreBiologies R data package that Mariathasan et al. provided (PMID:29443960). I have reached out to the corresponding author for clarification but do not received a response, so I was curious if you know the details on this matter.

Thank you!

Request for the RAW RNA-seq data and clinical data

Dear Tavi,

I am a urologist from Central South University. Recently, our team are doing a research to investigate the predictors of response to immune checkoints in bladder cancer. We want to validate our conclusions in some external immune-associated data set. We found that your data set was valuable and would give us great help.
Could you inform me if the raw RNA seq data and clinical information used in this analysis are publicly available for download somewhere?

Thanks,
Jiaohu

Genentech ID mismatch

For those not using the provided python code to load the data, note that the file tcga_subtypes_id_map.csv maps a genentech ID to a patient ID of 2397, even though that doesn't exist in clinical.csv. I believe this is a mismatch and that that patient ID should be 2937, which does exist in clinical.csv.