catcheR documentation

catcheR is a comprehensive bioinformatic package for designing and analyzing iPS2-seq experiments.

Contents:

• Getting started
  • Availability and Installation
  • Notes on obtaining iPS2-10X-seq, iPS2-CITE-seq, or iPS2-multi-seq Count Matrices
  • Notes on gene annotation
• catcheR_design - Oligonucleotide Design
• catcheR_step1QC - Pooled Cloning Step 1 QC
• catcheR_step2QC - Pooled Cloning Step 2 and hiPSC Genome Editing QC
• catcheR_scicounts - Obtain iPS2-sci-seq Count Matrices
• catcheR_10Xcatch - iPS2-10X-seq Perturbation Deconvolution
  • Step-by-step
• catcheR_10XcatchQC - Fine-Tune iPS2-10X-seq Perturbation Assignment
  • Step-by-step
• catcheR_filtercatch - Fine-Tune iPS2-10X-seq Perturbation Assignment
• catcheR_10Xnocatch - Identify cells expressing no shRNA
• catcheR_merge - Merge multiple samples
• caycheR_scicatch - iPS2-sci-seq perturbation deconvolution
• catcheR_scicatchQC - Fine-tune iPS2-sci-seq perturbation assignment
• catcheR_scinocatch - Identify cells expressing no shRNA in iPS2-sci-seq
• catcheR_sortcatch - Barcode reassignment
  • Steps
  • Arguments
  • Output
• catcheR_load - Data loading
  • Preparation
  • Running catcheR_load
  • Outputs
  • Compatibility
  • Next steps
• catcheR_pseudotime - Pseudotime
  • Step-by-step
  • Outputs
• catcheR_modules - Gene Modules
  • Step-by-step
  • Outputs
  • Integration with catcheR_pseudotime
• catcheR_enrichment - Enrichment / Depletion Analysis
  • Step-by-step
  • Arguments
  • Outputs