ribosome-profiling

There are 33 repositories under ribosome-profiling topic.

  • xryanglab/RiboCode

    release version

    Language:Python4644715
  • ribotricer

    smithlabcode/ribotricer

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

    Language:Python315558

  • zhpn1024/ribotish

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

    Language:Python243337

  • ribosomeprofiling/riboflow

    Pipeline for Ribosome Profiling Data

    Language:Groovy145279

  • Biochemistry1-FFM/uORF-Tools

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

    Language:Python13264

  • saketkc/riboraptor

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

    Language:Python13415

  • RickGelhausen/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:Python105314

  • sunyumail93/PipeRiboseq

    A comprehensive pipeline for Ribo-seq data analysis

    Language:Shell10212

  • smithlabcode/riborex

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

    Language:R915102

  • smithlabcode/ribotricer-results

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

    Language:Jupyter Notebook8450

  • Biobix/mQC

    Ribosome profiling mapping quality control tool

    Language:Python6712

  • fallerlab/Ribo-ODDR

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

    Language:Python6170

  • cgob/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:R4254

  • vimalkvn/riboplot

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

    Language:Python4211

  • celalp/ribofootprintR

    Fast data processing for ribosome footpring profiling experiments from bam files

    Language:R2100

  • jianhong/workshop2020

    workshop2020: Basic and advanced bioinformatics for RegenerationNEXT

    Language:R2201

  • saketkc/ribo-seq-snakemake

    Snakemake pipeline for Ribo-Seq analysis

    Language:Python220

  • jvandinter/container_pilot

    pilot pipeline that includes tool containerization

    Language:Shell1100

  • LewisLabUCSD/RibosomeProfiling

    Analyze ribosome profiling for organisms have ncbi annotation

    Language:Jupyter Notebook1202

  • MPUSP/snakemake-bacterial-riboseq

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

    Language:Python1070

  • rretkute/ML_gene_expression

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

    Language:Mathematica1200

  • ruggleslab/rivet

    Website source code for analysis of ribosome / polysome profiling

    Language:R1300

  • XuepengSun/RiboseqTools

    Tools for ribosome profiling

    Language:Perl1100

  • Biobix/mQC_galaxy

    Repo for the files needed for embedding mappingQC in the Galaxy environment

    Language:HTML0500

  • jvandinter/palomar-siles_et_al_2022

    Language:HTML0101

  • lcscs12345/riboss

    Comparison of the ability of open reading frames to recruit ribosomes within individual transcripts

    Language:Python0200

  • sudeepsahadevan/start_stop_analysis

    Workflow for Ribosome profiling data start and stop codon analysis.

    Language:Python0101

  • tjh48/riboSeqR

    Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.

    Language:R0200

  • vam-sin/riboclette

    Transformers for ribosome density prediction

    Language:Jupyter Notebook0100

  • xryanglab/RocA

    Reanalysis of ribosome profiling datasets reveals a novel function of rocaglamide A in perturbing the dynamics of translation elongation via eIF4A

    Language:Python0201

  • zhongyiwang1/Ribo-seq

    Pipeline and scripts for the comparative analysis of ribosome profiling and matched RNA sequencing data between organs and across species.

    Language:R0101

  • BIONF/PhyloRBF

    Language:R10

  • vam-sin/rb-prof

    machine learning algorithm for predicting ribosome densities at the gene level in different amino acid deprivation conditions

    Language:Python10