Calculate Genetic Interactions for Paired CRISPR Targets
Calculate Genetic Interaction scores
Check if internet/URL is available
Download and set up DepMap CN
Download and set up control genes
Refresh the annotation files by redownloading them
Refresh the example data files by redownloading them
Default creds path
Get file path to an default credentials RDS
Returns example data for package
Handler function for GET requests from Figshare
Annotate gimap data
A function to run filtering
Normalize Log fold changes
Make an empty gimap dataset object
Do tests --an internal function used by calc_gi() function
Get file path to an key encryption RDS
Pipe operator
Plot CRISPR scores after normalization
Expected vs Observed CRISPR Scatterplot
Rank plot for target-level GI scores
Target bar plot for CRISPR scores
Standardized plot theme
Volcano plot for GI scores
Create a CDF for the pgRNA normalized counts
Create a bar graph that shows the number of replicates with a zero cou...
Create a correlation heatmap for the pgRNA CPMs
Create a filter for pgRNAs which have a low log2 CPM value for the pla...
Filter out samples of zero counts Create a filter for pgRNAs which hav...
Create a histogram with plasmid log2 CPM values and ascertain a cutoff...
Create a histogram for the pgRNA log2 CPMs, faceted by sample
Create a histogram for the variance within replicates for each pgRNA
Run Quality Control Checks
Set up example count data
Set up example count data
Making a new gimap dataset
List the supported cell lines
Download and set up DepMap TPM data
Helps find meaningful patterns in complex genetic experiments. First gimap takes data from paired CRISPR (Clustered regularly interspaced short palindromic repeats) screens that has been pre-processed to counts table of paired gRNA (guide Ribonucleic Acid) reads. The input data will have cell counts for how well cells grow (or don't grow) when different genes or pairs of genes are disabled. The output of the 'gimap' package is genetic interaction scores which are the distance between the observed CRISPR score and the expected CRISPR score. The expected CRISPR scores are what we expect for the CRISPR values to be for two unrelated genes. The further away an observed CRISPR score is from its expected score the more we suspect genetic interaction. The work in this package is based off of original research from the Alice Berger lab at Fred Hutchinson Cancer Center (2021) <doi:10.1016/j.celrep.2021.109597>.