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KastanDay / ML4Bio

LLMs to execute Bioinformatics workflows, esp. RNA-seq
MIT License
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Create a full command line executable workflow for RNA-Seq on PBMC Samples. Open a new pull request (on a separate branch) and comment the PR number here when you're done. #4

Open KastanDay opened 1 year ago

KastanDay commented 1 year ago

Experiment Type: RNA-Seq Sequencing of total cellular RNA

Workflow Management: Bash/SLURM Scripting and job scheduling

Software Stack: FastQC MultiQC STAR RSEM samtools DESeq2

What else to know about the pipeline? I am working PBMC samples collected from patients that are undergoing immunotherapy.

Use the data files existing in Report_WholeBrain as input for this workflow.

You should write a series of bash scripts and R scripts that can accomplish this task. Open a PR with those scripts when you're done.

lil-jr-dev[bot] commented 1 year ago

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review. I'll comment if I get blocked or 'request your review' if I think I'm successful. So just watch for emails while I work. Please comment to give me additional instructions.

lil-jr-dev[bot] commented 1 year ago

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review. I'll comment if I get blocked or 'request your review' if I think I'm successful. So just watch for emails while I work. Please comment to give me additional instructions.

lil-jr-dev[bot] commented 1 year ago

Thanks for opening a new issue! I'll now try to finish this implementation and open a PR for you to review. I'll comment if I get blocked or 'request your review' if I think I'm successful. So just watch for emails while I work. Please comment to give me additional instructions.

lil-jr-dev[bot] commented 1 year ago

list index out of range

KastanDay commented 1 year ago

Here's the stack trace: https://smith.langchain.com/public/ccd521f4-3620-4d64-ada8-94ffe590c09f/r