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Broad transcriptomic dysregulation across the cerebral cortex in ASD

Code, data, and plots accompanying the manuscript.

To visualize gene and isoform expression data across diagnoses, regions, and sex, follow this link.

The 'main_datasets' directory includes main datasets and functional analysis summary plots of all gene and isoform modules.

File Notation:

PipelineStage_ScriptNumber_[OPTIONAL]Dataset_ScriptSection.extension

Pipeline Stages:

  1. RNAseq Processing
  2. DE Genes and Isoforms
  3. Transcriptomic Regional Identity (TRI) Analysis
  4. Weighted Gene Co-expression Network Analysis (WGCNA)
  5. Analysis of Regional Variation

Script Number:

Refers to the script within the pipeline stage. For example, for 'RNA Processing', Script #1 contains FASTQ file processing steps, whereas Script #2 contain quantified counts processing.

Dataset:

    A. Gene-level Expression
    B. Isoform-level Expression

If no dataset is indicated, the object applies to both datasets.

Script Section:

Section of the script where an object came from is indicated.