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riboseq

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zhpn1024 /ribotish

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

bam-files bioinformatics orfs ribosome-profiling translation-initiation-site riboseq

UpdatedDec 5, 2024
Python

schatzlab /scikit-ribo

Accurate estimation and robust modelling of translation dynamics at codon resolution

random-forest glmnet glm ridge-regression riboseq

UpdatedJun 27, 2017
Python

saketkc /riboraptor

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

bioinformatics snakemake genomics bioinformatics-pipeline ribosome-profiling riboseq

UpdatedMar 5, 2021
Python

XPRESSyourself /XPRESSpipe

An alignment and analysis pipeline for Ribosome Profiling and RNA-seq data

bioinformatics rna-seq pipeline genomics ngs profiling riboseq ribosome

UpdatedJul 2, 2024
Python

sunyumail93 /PipeRiboseq

A comprehensive pipeline for Ribo-seq data analysis

bioinformatics rna-seq translation pipeline ribosome-profiling riboseq ribosome-profiling-data ribo-seq

UpdatedMar 18, 2024
Shell

smithlabcode /riborex

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

ribosome-profiling riboseq differential-translation riborex

UpdatedApr 9, 2021
R

smithlabcode /ribotricer-results

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

translation ribosome-profiling riboseq orf-detection

UpdatedJan 8, 2021
Jupyter Notebook

fallerlab /Ribo-ODDR

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

bioinformatics rna-seq computational-biology bioinformatics-pipeline ribosome-profiling riboseq bioinformatics-scripts rrna oligonucleotide bioinformatics-tool oligo-design

UpdatedJan 27, 2023
Python

vimalkvn /riboplot

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

bioinformatics ngs ribosome-profiling riboseq bioinformatics-scripts

UpdatedAug 4, 2018
Python

noepozzan /small-peptide-pipeline

Pipeline for small peptide discovery

workflow bioinformatics pipeline nextflow profiling riboseq peptides ribosome

UpdatedDec 20, 2022
Nextflow

saketkc /ribo-seq-snakemake

Snakemake pipeline for Ribo-Seq analysis

snakemake ribosome-profiling riboseq

UpdatedMay 31, 2018
Python

junjunlab /riboTransVis

A Package for Ribosome Profiling Data Analysis

ggplot2 translation ribosome-profiling riboseq ribosome-occupancy-plot rna-coverage-plot

UpdatedMar 24, 2025
R

MPUSP /snakemake-bacterial-riboseq

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

workflow snakemake conda singularity bioinformatics-pipeline ribosome-profiling riboseq

UpdatedFeb 2, 2025
Python

ms-gx /CircAidMe

CircAidMe is a tool designed to analyze data generated with CircAID-p-seq (immaginabiotech.com/product/circaid-p-seq/). CircAidMe was designed and implemented by Genexa (genexa.ch) in collaboration with Immagina Biotechnology.

transcriptomics riboseq oxfordnanopore rna-footprinting

UpdatedFeb 4, 2021
C++

Lukas-Wierdsma /Internship-UCC-2023

Repository for my internship at the University College Cork in 2023.

quality-control riboseq

UpdatedMay 24, 2023
Jupyter Notebook

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