Bioinformatics – NeuroBorder

Retrieve high-confidence NDD genes

NDD

gene

Retrieve high-confidence NDD genes from various databases.

Bulk RNA-Seq differential expression analysis and batch correction with DESeq2, limma, or sva

bulk rna-seq

differential expression

batch correction

deseq2

limma

sva

Perform batch correction with DESeq2, limma, or sva.

Build ENCODE ATAC/ChIP-Seq pipeline indices

encode

atac-seq

chip-seq

index

For more details, refer to ENCODE ATAC-Seq pipeline from GitHub, ENCODE ATAC-Seq pipeline from Google doc, ENCODE ChIP-Seq pipeline from GitHub, and ENCODE ChIP-Seq pipeline…

Build ENCODE RNA-Seq pipeline indices

encode

rna-seq

index

For more details, refer to ENCODE RNA-Seq pipeline.

DE-related analysis for bulk proteomics

bulk proteomics

differential expression

At present, this pipeline only allows two sample groups contained in your input files.

MPRA analysis pipeline

mpra

Before running any of the following steps, you should rename your FASTQ files according to these rules.

Misc R code

r

misc

Used to collect various R code snippets.

Cut&Tag analysis pipeline

cut&tag

Before running any of the following steps, you should rename your FASTQ files according to these rules.

Agilent mRNA microarray analysis using limma

agilent

mrna

microarray

limma

A little example for how to use limma to analyze Agilent mRNA microarray data.

Identify housekeeping genes

bulk rna-seq

housekeeping genes

In brief, housekeeping genes are those with higher expression levels, low variances, and ubiquitous expression profiles across samples and species.

Bulk RNA-seq pseudotime analysis

bulk rna-seq

pseudotime

In scRNA-seq, various tools, such as Monocle3, provide the capability of performing pseudotime analysis. In brief, assume that there are both progenitors and more…