riboStreamR

Please Choose Your RNA-seq BAM Files

Browse...

Please Choose Footprinting BAM Files

Browse...

Please Choose Annotation File

Browse...

Choose the Species

Subsample 100K reads?

Keep reads for genes:

Bringing Your Sequencing Data to Life

Welcome to riboStreamR , a platform for ribo-seq data analysis.

Get started by uploading your files in the panel to the left and hitting Preprocess.

Once you recieve conifrmation below that your files have been successfully uploaded and processed, you can move onto viewing our collection of QC plots, which are available in the tabs above.

Choose the Experiment Type

Choose the Strands

Choose which Mapped Types

Choose which Features

Choose which Features to Separate

Choose which Frames

Choose the Factor to Separate Lines

Choose the Factor to Separate Plots

Choose Smoothing Bandwidth

Select X axis min

Select X axis max

Choose your color palette

Choose the Experiment Type

Choose the Strands

Choose which Mapped Types

Choose which Features

Choose which Features to Separate

Choose Read Length Range

Choose which Frames

Choose the Factor to Separate Bars

Choose the Factor to Separate Colors

Choose the Factor to Separate Groups

Choose the Factor to Separate Plots

Choose your color palette

Notes

Download

Choose the Experiment Type

Choose the strands

Choose Read Length Range

Choose which Mapped Types

Choose which Features

Choose which Features to Separate

Choose which Frames

Choose the Factor to Separate Lines

Choose the Factor to Separate Plots

Choose your color palette

Download

Choose the Experiment Type

Choose the Strands

Choose which Mapped Types

Choose which Features

Choose Read Length Range

Choose which Frames

Choose which Features Columns to Include

Choose the Experiment Type

Choose the Strands

Choose which Mapped Types

Choose Read Length Range

Choose which Frames

Choose your window size

Choose the Factor to Separate Lines

Choose your color palette

Download

Choose the Experiment Type

Choose the Strands

Choose which Mapped Types

Choose Read Length Range

Choose which Frames

Choose the Factor to Separate Lines

Choose the Factor to Separate Plots

Download

Choose the Experiment Type

Choose the Strands

Choose which Mapped Types

Choose Read Length Range

Choose your window size

Choose the Factor to Separate Plots

Choose your color palette

Download

Choose the Experiment Type

Choose the Strands

Choose which Mapped Types

Choose which Features

Choose Read Length Range

Choose how to separate groups

Choose your color palette

Choose which Frames

Download

Type of differential analysis:

Which Experiment Types

How many different Treatments?

Please Choose Annotation GFF3 File

Browse...

Download Counts Download RPKMs Download edgeR

Choose Plots

Summary Table

Read Length Distribution

GC Distribution

Feature Components

Meta Gene

Gene Viewer

Meta Periodicity

Periodicity

Differential

Generate

QC Report Generator

Choose which plots to include in your report using the panel to the left and press Generate

to create the report.

Forward Scan Threshold

Forward Scan Window Size

Forward Scan Influence

Reverse Scan Threshold

Reverse Scan Window Size

Reverse Scan Influence

Centralized Scan Threshold

Centralized Scan Window Size

Centralized Scan Influence

Pilot Data

Please upload your count file

Browse...

RNA treatment 1 Columns

RNA treatment 2 Columns

RPF treatment 1 Columns

RPF treatment 2 Columns

Number of genes to simulate

Percentage genes with differential translation efficiency

Meaningful effect size

Adjusted p-value

Number of repetitions

Differential analysis tool

Figures

Bringing Your Count Data to Life

Welcome to riboSimR , a platform for RNA-seq and Ribo-seq data simulation and power analysis.

Get started by uploading a count file and entering which columns correspond to your samples.

Use the toolbar to select the desired parameters for your simulations. The Figures field is used to choose which set of plots to display. The acronyms in the figure titles stand for:

DTE - Differential translation efficiency; DE - Differential expression; DT - Differential translation; TP - Number of true positives; FDC - False discovery cost.

Press Simulate to begin the simulation and plot generation process, which may take up to thirty minutes per figure.