BED2txDb |
Bedgraph to TranscriptDb object |
bedgraph2norm |
Import bedgraph to GRanges |
comp |
Arranging information from GRanges produced by readsamples() on per position (nucleotide) basis. |
compdata |
Create or extend norm_GR GRanges using Comp_GR GRanges |
correct_oversaturation |
Correcting EUC of oversaturated fragments. |
dtcr |
Calculate deltaTCR. |
GR2norm_df |
Export normalized GRanges object to data frame |
k2n_calc |
Calculate number of Estimated Unique Counts (EUC's) corresponding to given number of observed unique barcodes. |
norm2bedgraph |
Exporting data in norm_df data frame (product of dtcr, slograt and swinsor) to bedgraph format compatible with UCSC Genome Browser |
norm_df2GR |
Function to convert norm_df data frame (product of GR2norm_df()) to GRanges. |
plotReads |
Plotting ranges from GRanges |
plotRNA |
Plot normalized values over transcript positions |
readsamples |
Import of tables prepared by Galaxy workflow to R environment |
slograt |
Smooth Log2-ratio |
swinsor |
Smooth Winsorization |
swinsor_vector |
Smooth Winsor Normalization |
winsor |
Winsor normalization with fitting to <0,1> range. |