ribosome-profiling
There are 5 repositories under ribosome-profiling topic.
- Language:Python 51
zhpn1024 / ribotish
Ribo-seq TIS Hunter, predicting translation initiation sites and ORFs using riboseq data
Language:Python 38- ribotricer
smithlabcode / ribotricer
A tool for accurately detecting actively translating ORFs from Ribo-seq data
Language:Python 36 ribosomeprofiling / riboflow
Pipeline for Ribosome Profiling Data
Language:Groovy 16Biochemistry1-FFM / uORF-Tools
uORF-Tools are a workflow and a collection of tools for the analysis of 'Upstream Open Reading Frames' (short uORFs)
Language:Python 13saketkc / riboraptor
Tool for ribo-seq analysis. Most of the functionality moved to ribotricer (https://github.com/smithlabcode/ribotricer)
Language:Python 13RickGelhausen / HRIBO
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, and integrates them with additional computed features. This facilitates both the rapid discovery of ORFs and their prioritization for functional characterization.
Language:Python 11Riborex: Fast and flexible identification of differential translation from Ribo-seq data
Language:R 10sunyumail93 / PipeRiboseq
A comprehensive pipeline for Ribo-seq data analysis
Language:Shell 10Results and scripts for benchmarking ribotricer for translating ORF detection from Ribo-seq data
Language:Jupyter Notebook 8- Language:Python 6
fallerlab / Ribo-ODDR
Ribo-seq focused Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs
Language:Python 5cgob / codonDT_snakemake
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).
Language:R 4vimalkvn / riboplot
RiboPlot includes programs to plot and output Ribo-Seq read counts from an alignment file (BAM format).
Language:Python 4celalp / ribofootprintR
Fast data processing for ribosome footpring profiling experiments from bam files
Language:R 2jianhong / workshop2020
workshop2020: Basic and advanced bioinformatics for RegenerationNEXT
Language:R 2junjunlab / riboTransVis
A Package for Ribosome Profiling Data Analysis
Language:R 2MPUSP / snakemake-bacterial-riboseq
Bacterial-Riboseq: A Snakemake workflow for the analysis of riboseq data in bacteria.
Language:Python 2Snakemake pipeline for Ribo-Seq analysis
Language:Python 2jvandinter / container_pilot
pilot pipeline that includes tool containerization
Language:Shell 1LewisLabUCSD / RibosomeProfiling
Analyze ribosome profiling for organisms have ncbi annotation
Language:Jupyter Notebook 1rretkute / ML_gene_expression
Mathematica notebook to compare methods of ML for ribosom density on mRNA prediction
Language:Mathematica 1ruggleslab / rivet
Website source code for analysis of ribosome / polysome profiling
Language:R 1xryanglab / RocA
Reanalysis of ribosome profiling datasets reveals a novel function of rocaglamide A in perturbing the dynamics of translation elongation via eIF4A
Language:Python 1- Language:Perl 1
Biobix / mQC_galaxy
Repo for the files needed for embedding mappingQC in the Galaxy environment
Language:HTML 0- Language:HTML 0
lcscs12345 / riboss
Comparing translation of open reading frames within individual transcripts
Language:Python 0sudeepsahadevan / start_stop_analysis
Workflow for Ribosome profiling data start and stop codon analysis.
Language:Python 0tjh48 / riboSeqR
Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.
Language:R 0vam-sin / riboclette
Transformers for ribosome density prediction
Language:Jupyter Notebook 0zhongyiwang1 / Ribo-seq
Pipeline and scripts for the comparative analysis of ribosome profiling and matched RNA sequencing data between organs and across species.
Language:R 0- Language:R
machine learning algorithm for predicting ribosome densities at the gene level in different amino acid deprivation conditions
Language:Python
