COTAN documentation

Overview

This web page contains all data regarding the COTAN paper. Here can be found:

• All datasets analysis, some of which with and whitout initial cleaning step.

• The comparison of our gene clustering to detect cortex layer markers, with the markers found in Loo et al. paper. This part also contains the comparison with a WGCNA approach.

• The negative dataset analysis.\

• The repository for the package tool is the gitHub.

Datasets

In this work where use the following public datasets:

• Mouse embryonic cortex dataset with four time points of development: E11.5 (GSM2861510), E13.5 (GSM2861511), E15.5 (GSE107122), E17.5 (GSM2861514). This study was performed by the Drop-seq scRNAseq technology.
• Mouse dentate gyrus dataset (GSE104323) with many different time points of development but, for this study, only the E16.5 was used. This study was performed using the 10X platform.
• Mouse embryonic cortex dataset (GSE123335) with two time points of development: E14.5 and P0. In this case the method used was Drop-seq.

Computation time

The COTAN analysis time is approximatively proportional to the cell number in the dataset. In particular, the most demanding step is the analysis step when a is minimized for each gene. This step is done by a multicore function (that is not supported under windows architecture). By default, and during tests it was fixed to 11 cores. For example, a dataset with around 5000 cells was analysed in around 3 minutes. The machine used had RAM 64GiB and an Intel(R) Dual Xeon(R) Silver 4214 CPU @ 2.20GHz.

• For more details see the specific page.

date()

## [1] "Wed Jan 19 10:08:52 2022"