Single cell analysis of Cancer

Question

[moustafa_abohawya]

I need help to identify which tools/databases to start from.

So here is what I want to do.

I want to analyze single cell seq data for colorectal or gastric cancer cohorts.

In each patient, I need to identify cluster of cells with low expression of a specific gene marker, estimate the ratio of these cells in each tumor single sequenced and potentially correlate this ratio with clinical data about the patients it comes from.

I know it is almost a whole study, but I need at least a starting point.

There are hundreds of single cell tool at the moment. But I don't know from where to start

Thanks in advance

[ATpoint]

I don't see how this could be answered. You're essentially asking people to do all your work as you neither give datasets nor show what you tried. It's unusual to analyse single-cell per patient rather than doing some sort of integration. Often you won't have lots of patient details due to privacy reasons.

[GenoMax]

I want to analyze single cell seq data for colorectal or gastric cancer cohorts

It is possible that you have data in hand (otherwise this would be difficult to do owing to the patient privacy issue mentioned) but your post is not very clear about the data availability.

I need help to identify which tools/databases to start from.

Assuming you have the data then OSCA (https://bioconductor.org/books/release/OSCA/ ) and Seurat (https://satijalab.org/seurat/articles/get_started_v5_new ) are the go to open-source software options for all things single cell.

There are commercial options like Partek Flow and CLC genomics but they will require a purchase.

[Ram]

How do you foresee getting your hands on data of this detail and depth?