Package index • deseq2pip

Pipeline Functions

run_rna_pip(): Run Complete RNA-seq Pipeline

run_atac_pip(): Run Complete ATAC-seq Pipeline

deseq2pip-package: DESeq2 Pipeline for RNA-seq Analysis

enrichmentmap_pip(): Format Enrichment Map Data

plot_peak_annot_pip(): Plot ATAC-seq Peak Annotation

run_diffexp_pip(): Run Differential Expression Pipeline

run_dist_pip(): Run Sample Distance Pipeline

run_gsea_pip(): Run GSEA pipeline

run_qc_pip(): Run Quality Control Pipeline

write_cls_pip(): Write class file pipeline for EnrichmentMap

Wrapper Functions

run_diffexp_wrapper(): Run Differential Expression Wrapper

run_gsea_wrapper(): Run GSEA wrapper

Quality Control (Module 1)

remove_low_expression(): Remove Genes with Low Expression

remove_mt_genes(): Remove Mitochondrial Genes from DESeq2 Object

remove_xy_genes(): Remove XY Chromosome Genes from DESeq2 Object

check_library(): Check Library Size Distribution

run_batch_correction(): Run batch correction by Limma

validate_batch(): Validate batch

run_pca(): Run Principal Component Analysis

run_distance(): Calculate and Plot Sample Distances

Differential Expression (Module 2)

read_diffexp(): Read Differential Expression Results

run_diffexp(): Run Differential Expression Analysis

run_diffexp_pip(): Run Differential Expression Pipeline

run_diffexp_wrapper(): Run Differential Expression Wrapper

Gene Set Enrichment Analysis (Module 3)

plot_gsea_barplot(): Plot GSEA Results

plot_gsea_enriched(): Plot GSEA Enriched Plot

read_gsea_rds(): Read GSEA Results from RDS Files

read_gsea_tsv(): Read GSEA Results from TSV Files

run_gsea(): Run Gene Set Enrichment Analysis

run_gsea_pip(): Run GSEA pipeline

run_gsea_wrapper(): Run GSEA wrapper

validate_gsea(): Validate gsea

validate_gsea_comparison(): Validate gsea for comparison

validate_gsea_object(): Validate gsea object

enrichmentmap_pip(): Format Enrichment Map Data

write_cls(): Write class file pipeline for EnrichmentMap

write_cls_pip(): Write class file pipeline for EnrichmentMap

Plot Functions (Module 4)

plot_gene_exprs(): Plot Gene Expression

plot_gsea_barplot(): Plot GSEA Results

plot_gsea_enriched(): Plot GSEA Enriched Plot

plot_ma(): Generate MA Plot

plot_peak_annot(): Plot ATAC-seq Peak Annotations

plot_peak_annot_pip(): Plot ATAC-seq Peak Annotation

plot_pie_chart(): Create Pie Chart for ATACseq Annotation

plot_volcano(): Generate Volcano Plot

Helper Functions

import_msigdbr(): Import MSigDB Gene Sets

import_nfcore_atac(): Import nfcore ATAC-seq DESeq2 Object

import_nfcore_rna(): Import nfcore/rnaseq DESeq2 Object

getTSS(): Get TSS peaks from DESeq2 object

summarize_genes_dds(): Summarize Gene Expression in DESeq2 Object

generate_comparisons(): Generate Comparison Names

validate_dds_comparison(): Validate DESeq2 object for comparison

validate_gsea_comparison(): Validate gsea for comparison

validate_res_comparison(): Validate differential expression results for comparison

Validation Functions

validate_batch(): Validate batch

validate_dds(): Validate DESeq2 object

validate_dds_atac(): Validate DESeq2 object for ATAC-seq

validate_dds_comparison(): Validate DESeq2 object for comparison

validate_dds_group_by(): Validate DESeq2 object for RNA-seq

validate_gene_set(): Validate gene set

validate_gsea(): Validate gsea

validate_gsea_comparison(): Validate gsea for comparison

validate_gsea_object(): Validate gsea object

validate_logical(): Validate logical

validate_method(): Validate methods

validate_msigdbr(): Validate msigdbr

validate_order(): Validate order

validate_org(): Validate organism

validate_pals(): Validate pals

validate_paths(): Validate paths

validate_quantile(): Validate quantile

validate_res(): Validate differential expression results

validate_res_comparison(): Validate differential expression results for comparison

validate_shape(): Validate shape

Save Functions

save_expression(): Save Expression Data from DESeq2 Object

save_plot(): Save ggplot Object as PDF

save_tsv(): Save Data Frame as TSV File

Logging Functions

log_output(): Log output

log_renv(): Log renv Snapshot