QMSFC

Data and code for the Multiomics surface receptor profiling of the NCI-60 tumor cell panel uncovers novel theranostics for cancer immunotherapy paper.

Clone this repository

We can clone via:

git clone git@github.com:qbicsoftware/QMSFC.git

If the following error is appearing:

Error downloading object: Curate_ArrayData_April2022/GSE32474_series_matrix.txt (b9a6057): Smudge error: Error downloading Curate_ArrayData_April2022/GSE32474_series_matrix.txt (b9a6057e68823732e88825d5bd2d62236342bab40cb6d59bacbc25ced9783bc8): batch response: This repository is over its data quota. Account responsible for LFS bandwidth should purchase more data packs to restore access.

Errors logged to /home/heumos/QBiC/QMSFC/.git/lfs/logs/20240425T101004.638820054.log
Use `git lfs logs last` to view the log.
error: external filter 'git-lfs filter-process' failed
fatal: Curate_ArrayData_April2022/GSE32474_series_matrix.txt: smudge filter lfs failed
warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry with 'git restore --source=HEAD :/'

Then please follow the guidance given at https://stackoverflow.com/questions/62905325/this-repository-is-over-its-data-quota-account-responsible-for-lfs-bandwidth-sh to fork and archive this repository and downlaod it as ZIP.

Then change your directory:

cd QMSFC

Install basic required software

Some basic software is required in order to run the R analysis scripts. Please install Rstudio as described in https://www.rstudio.com/products/rstudio/download/#download. To get a miniconda installation please follow https://conda.io/projects/conda/en/latest/user-guide/install/index.html.

Prepare conda environments QMSFC and QMSFC_2

Once you have installed miniconda you can add the QMSFC environment as follows:

conda env create -f QMSFC_environment_21042022.yml

For the QMSFC_2 environment, you have to execute:

conda env create -f QMSFC_environment_22042022.yml

Run quality control analysis

Ensure that you are in the QMSFC environment:

conda activate QMSFC

For Rstudio to work properly, we tell it the path to th R version used in the conda environment:

export RSTUDIO_WHICH_R=~/miniconda3/envs/QMSFC/bin/R

If you installed miniconda to a different location than your home folder, please adjust the path above.

Now open Rstudio from the command line:

rstudio

Depending on your OS, it may also be rstudio-bin.

Navigate to File and click on Open File.... Navigate to the IsotypeControl_QC folder and open IsotypeControl_QC.R. Select all lines and press SHIFT+ENTER in order to re-run the analysis.

Run pairwise correlation analysis for cell lines measured in 2 weeks

Ensure that you have the QMSFC environment activated and Rstudio is open as in Run quality control analysis.

Navigate to File and click on Open File.... Navigate to the week1_week2 folder and open week1_week2.R. Select all lines and press SHIFT+ENTER in order to re-run the analysis.

Run homogenize identifiers script

Ensure that you have the QMSFC environment activated and Rstudio is open as in Run quality control analysis.

Navigate to File and click on Open File.... Navigate to the Homogenize_Identifiers folder and open harmonize_IDs.R. Select all lines and press SHIFT+ENTER in order to re-run the analysis.

Run Tx curation

Ensure that you are in the QMSFC_2 environment:

conda activate QMSFC_2

For Rstudio to work properly, we tell it the path to th R version used in the conda environment:

export RSTUDIO_WHICH_R=~/miniconda3/envs/QMSFC_2/bin/R

If you installed miniconda to a different location than your home folder, please adjust the path above.

Now open Rstudio from the command line:

rstudio

Depending on your OS, it may also be rstudio-bin.

Navigate to File and click on Open File.... Navigate to the Curate_ArrayData_April2022 folder and open curate_array_April2022.R. Select all lines and press SHIFT+ENTER in order to re-run the analysis.

Run Px curation

Ensure that you have the QMSFC_2 environment activated and Rstudio is open as in Run Tx curation.

Navigate to File and click on Open File.... Navigate to the Curate_Px_April2022 folder and open curate_px_gholami_April2022.R. Select all lines and press SHIFT+ENTER in order to re-run the analysis.

Run MCIA analysis

Ensure that you have the QMSFC environment activated and Rstudio is open as in Run quality control analysis.

Navigate to File and click on Open File.... Navigate to the multiomics_March2022_NO_LOX_NO_ISOTYPE_CONTORLS folder and open omicade4_March2022_NO_LOX_NO_ISOTYPE_CONTROLS.R. Select all lines and press SHIFT+ENTER in order to re-run the analysis.

Run Recount2 analysis

For each of the folders starting with recount2 you can run the same analysis steps. In the following an example for COLON.

Ensure that you have the QMSFC_2 environment activated and Rstudio is open as in Run Tx curation.

Navigate to File and click on Open File.... Navigate to the recount2_co_April2022 folder and open curate_px_gholami_April2022.R. Select all lines and press SHIFT+ENTER in order to re-run the analysis.