release version

A tool for accurately detecting actively translating ORFs from Ribo-seq data

Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data

Pipeline for Ribosome Profiling Data

uORF-Tools are a workflow and a collection of tools for the analysis of 'Upstream Open Reading Frames' (short uORFs)

Tool for ribo-seq analysis. Most of the functionality moved to ribotricer (https://github.com/smithlabcode/ribotricer)

A comprehensive pipeline for Ribo-seq data analysis

Riborex: Fast and flexible identification of differential translation from Ribo-seq data

We present HRIBO (High-throughput annotation by Ribo-seq), a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data. The workflow performs all required pre-processing steps and quality control. Importantly, HRIBO outputs annotation-independent ORF predictions based on two complementary prokaryotic-focused tools, …

Results and scripts for benchmarking ribotricer for translating ORF detection from Ribo-seq data

Ribosome profiling mapping quality control tool

Ribo-seq focused Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs

Ribo-DT is a snakemake pipeline to infer single-codon and codon-pair dwell times as well as gene flux from ribosome profiling data using generalized linear model (GLM) with negative binomial noise model (Gobet et al., PNAS, 2020).

RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format).

Snakemake pipeline for Ribo-Seq analysis

Fast data processing for ribosome footpring profiling experiments from bam files

Bacterial-Riboseq: A Snakemake workflow for the analysis of riboseq data in bacteria.

workshop2020: Basic and advanced bioinformatics for RegenerationNEXT

pilot pipeline that includes tool containerization

Mathematica notebook to compare methods of ML for ribosom density on mRNA prediction