Introducing the CDS Blog

Welcome

Working with MIX-Seq data

We recently published a new method called MIX-Seq. This post will get you started analyzing MIX-Seq data using R and Seurat

The MON artifact

Identification and consequences of an artifact in Project Achilles

Assessing Confidence in Achilles Gene Profiles

A long post which contains both an explanation of how we calculate gene confidence scores together with the code we use to do so.

Speeding up calculation of Pearson correlation for matrices with missing data

It's easy enough to calculate pearson correlation efficiently using numpy, but what if you have missing values in your data?

Library permutation leads to overly optimistic p-values in CRISPR screens

Permuting reagent labels is a common approach to generate null distributions in CRISPR screens. This post discusses the problems with this method and suggests an alternative.

Genes with no unique* sgRNAs are being dropped

Problem with and solution for multi-gene targeting sgRNAs

When not to use Spearman correlations

Spearman correlations are frequently used in computational biology, but for a common class of biological relationships Pearson is a better choice.