|
BbcEdgeR-class
|
BbcEdgeR, a class for storing an edgeR analysis |
|
BbcEdgeR()
|
Constructor for BbcEdgeR |
|
BbcSE-class
|
BbcSE, an extension of SummarizedExperiment for VAI BBC RNA-seq workflow |
|
BbcSE()
|
Constructor for BbcSE |
|
`aln_metrics<-`()
|
Setter for aln_metrics slot |
|
aln_metrics()
|
Getter for aln_metrics slot |
|
batch_correct_norm_cts()
|
Batch correct normalized counts |
|
bbcRNA
|
bbcRNA: Bulk RNA-seq workflow for VAI BBC.. |
|
cbind(<BbcSE>)
|
Column combining method for BbcSE |
|
`de_results<-`()
|
Setter for de_results slot in a BbcEdgeR object |
|
de_results()
|
Getter for de_results slot from BbcEdgeR object |
|
deseq2()
|
Getter for deseq2 slot |
|
`dgelist<-`()
|
Setter for dgelist slot in a BbcEdgeR object |
|
dgelist()
|
Getter for dgelist slot from BbcEdgeR object |
|
`edger<-`()
|
Setter for edger slot |
|
edger()
|
Getter for edger slot |
|
ens2entrez()
|
Convert Ensembl IDs to Entrez IDs for gene enrichment analyses. |
|
ens2sym()
|
Convert Ensembl IDs to gene symbols. |
|
findDEGs()
|
Identify DE genes. |
|
find_missing_in_gseaResult()
|
Compare genes in clusterProfiler gseaResult to genes in a bbcRNA object |
|
get_de_table()
|
Get a table of DE results |
|
lists_to_edger_contrasts()
|
Function to convert to edgeR-style contrasts |
|
makeDGEList()
|
Make a DGEList object. |
|
`norm_cts<-`()
|
Setter for norm_cts slot in a BbcEdgeR object |
|
norm_cts()
|
Getter for norm_cts slot from BbcEdgeR object |
|
normalize_counts()
|
Calculate normalized counts. |
|
plot_PCA()
|
PCA, screeplot and PERMANOVA test |
|
plot_aln_metrics()
|
Plot alignment metrics |
|
plot_heatmap()
|
Plot heatmap |
|
plot_pval_distrib()
|
Plot P-values |
|
plot_volcano()
|
Volcano plot |
|
prep_clusterprofiler_genelist()
|
Prep clusterProfiler geneList |
|
rbind(<BbcSE>)
|
Row combining method for BbcSE |
|
read_col_meta()
|
Read column meta data |
|
read_star_aln_metrics()
|
Import STAR Log.final.out files for analyzing mapping rates. |
|
run_gsea()
|
Run GSEA |
|
run_hypergeometric()
|
Run hypergeometric test |
|
searchBM()
|
Search biomart datasets with keyword |
|
shorten_desc()
|
Shorten Description names from ClusterProfiler results. |
|
show(<BbcSE>)
|
show method for BbcSE |
|
star_to_mat()
|
Convert STAR read counts to count matrix. |
|
`[`(<BbcSE>,<ANY>,<ANY>,<ANY>)
|
Subsetting method for BbcSE |
|
`[<-`(<BbcSE>,<ANY>,<ANY>,<BbcSE>)
|
Assigning subsets method for BbcSE |