RIMA_pipeline
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liulab-dfci
Hi - Following the information listed in [Chapter6.7.2](https://liulab-dfci.github.io/RIMA/Infiltration.html#starting-with-tpm-matrix) and having an issue with the code because there is no information on where 'plotfunction.R' came from. Can you provide me the...
Hi， I tried to install RIMA environment. However, I found out that I could not install two python module (mhcnuggets==2.3.3, mhctools==1.8.1). Other necessary module and packages were installed successfully and...
hello running the following command resulted in the following error: ~/RIMA_pipeline$ snakemake -s RIMA.snakefile -np Building DAG of jobs... MissingInputException in line 96 of modules/mutation/mutation_cohort.snakefile: Missing input files for rule...
I have installed the package as detailed in the Tutorial of RNA-seq tumor immunity analysis using Google Cloud Platform on my institute’s HPC. The pipeline completes the star aligning, salmon...
Dear, I am wondering how to get Ig isotype frequency as your tutorial, I guess to run get.bcr.cluster.classswitch funtion in trust4_bcr_process.R? Thank you so much!
Hi, thanks for this tool. I was wondering whether I can skip read alignment step and directly perform gene quantification and DEG analysis, which are all I want to do....
Hi I want to apply the function you kindly provided, but was running into some issues of using my own data, probably due to the format. Can you please provide...
Hello, I have been trying to use the Immune_repertoire portion of the RIMA pipeline to calculate SHM statistics for TRUST4 output mouse data (that has not otherwise been processed through...
Hi there, thank you for the great and detailed package! I was wondering if you could help me resolve an error with the pipeline where the process is killed before...
Good afternoon, thank you very much for making the tool available. I have installed RIMA following the GitHub tutorial (AWS), I have the following error when trying to run snakemake...
