isomiRs-package |
isomiRs |
counts |
Accessors for the count matrix of a IsomirDataSeq object. |
counts-method |
Accessors for the count matrix of a IsomirDataSeq object. |
counts.IsomirDataSeq |
Accessors for the count matrix of a IsomirDataSeq object. |
counts<--method |
Accessors for the count matrix of a IsomirDataSeq object. |
dat286.long |
Data frame containing mirna from Argyropoulos's paper |
design |
Accessors for the 'design' slot of a IsomirDataSeq object. |
design-method |
Accessors for the 'design' slot of a IsomirDataSeq object. |
design<--method |
Accessors for the 'design' slot of a IsomirDataSeq object. |
ego |
enrichResult class |
findTargets |
Find miRNAs target using mRNA/miRNA expression |
gene_ex_rse |
Data frame containing gene expression data |
isoAnnotate |
Annotate the rawData of the IsomirDataSeq object |
isoCounts |
Create count matrix with different summarizing options |
isoDE |
Differential expression analysis with DESeq2 |
IsomirDataSeq |
Class that contains all isomiRs annotation for all samples |
IsomirDataSeq-class |
Class that contains all isomiRs annotation for all samples |
IsomirDataSeqFromFiles |
Loads miRNA annotation from seqbuster tool or pre-processed data. |
IsomirDataSeqFromMirtop |
Import 'mirtop' output into 'IsomirDataSeq' |
IsomirDataSeqFromRawData |
Loads miRNA annotation from seqbuster tool or pre-processed data. |
isomiRs |
isomiRs |
isoNetwork |
Clustering miRNAs-genes pairs in similar pattern expression |
isoNorm |
Normalize count matrix |
isoPlot |
Plot the amount of isomiRs in different samples |
isoPlotNet |
Functional miRNA / gene expression profile plot |
isoPlotPosition |
Plot nucleotides changes at a given position |
isoPLSDA |
Partial Least Squares Discriminant Analysis for 'IsomirDataSeq' |
isoPLSDAplot |
Plot components from isoPLSDA analysis (pairs plot) |
isoSelect |
Method to select specific miRNAs from an IsomirDataSeq object. |
isoSelect-method |
Method to select specific miRNAs from an IsomirDataSeq object. |
isoSelect.IsomirDataSeq |
Method to select specific miRNAs from an IsomirDataSeq object. |
isoTop |
Heatmap of the top expressed isomiRs |
ma_ex |
Data frame containing gene-mirna relationship |
mirData |
Example of IsomirDataSeq with human brain miRNA counts data |
mirna2targetscan |
Find targets in targetscan database |
mirna_ex_rse |
Data frame containing mirna expression data |
mirTritation |
Data frame containing mirna from Argyropoulos's paper |
updateIsomirDataSeq |
Update IsomirDataSeq object from version < 1.7 |