From b4019539e2190d6f474ac2492c04f881c9816516 Mon Sep 17 00:00:00 2001 From: abearab Date: Sat, 22 Jun 2024 02:26:44 -0700 Subject: [PATCH] add `GuideCounter` to README --- README.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 0c26756..3f36e84 100644 --- a/README.md +++ b/README.md @@ -59,15 +59,15 @@ A minor novelty here has enabled processing single, dual, or multiple sgRNA CRISPR screens. Also, this approach can retain recombination events which can occur in dual or higher order sgRNA CRISPR screens. -Currently, `Counter` class from the `ngs` module can process FASTQ files and generate counts for standard +Currently, `GuideCounter` class from the `ngs` module can process FASTQ files and generate counts for standard CRISPR screens with [single](#dcas9-crisprai-single-sgrna-screens) or [dual](#crispri-dual-sgrna-screens) guide design. Here is a draft code to process FASTQ files and generate counts for an experiment with [CRISPRi-dual-sgRNA-screens](#crispri-dual-sgrna-screens): ```python -# Initialize the Counter object -counter = scp.Counter(cas_type = 'cas9', library_type = 'single_guide_design') +# Initialize the GuideCounter object +counter = scp.GuideCounter(cas_type = 'cas9', library_type = 'single_guide_design') # Load the reference library counter.load_library("", sep = '\t', verbose = True, index_col=None) @@ -90,7 +90,7 @@ Here is a draft code to process FASTQ files and generate counts for an experimen ```python # Initialize the Counter object -counter = scp.Counter(cas_type = 'dCas9', library_type = 'dual_guide_design') +counter = scp.GuideCounter(cas_type = 'dCas9', library_type = 'dual_guide_design') # Load the reference library counter.load_library("", sep = '\t', verbose = True, index_col=None) @@ -108,7 +108,7 @@ counter.get_counts_matrix( ) ``` -After this, you have `.counts_mat` calculated in the `Counter` object. +After this, you have `.counts_mat` calculated in the `GuideCounter` object. ___