junjunlab/riboTransVis

A Package for Ribosome Profiling Data Analysis

Language: R - Size: 4.48 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 9 - Forks: 0

lcscs12345/riboss

Comparing translation of open reading frames within individual transcripts

Language: Python - Size: 262 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 0 - Forks: 1

smithlabcode/ribotricer

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

Language: Python - Size: 50.1 MB - Last synced at: 10 days ago - Pushed at: 3 months ago - Stars: 37 - Forks: 8

vam-sin/riboclette

Transformers for ribosome density prediction

Language: Jupyter Notebook - Size: 137 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0

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: Python - Size: 2.66 MB - Last synced at: 10 days ago - Pushed at: about 1 month ago - Stars: 11 - Forks: 4

zhpn1024/ribotish

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

Language: Python - Size: 262 KB - Last synced at: 5 days ago - Pushed at: 5 months ago - Stars: 38 - Forks: 9

xryanglab/RiboCode

release version

Language: Python - Size: 301 KB - Last synced at: 16 days ago - Pushed at: almost 3 years ago - Stars: 51 - Forks: 16

MPUSP/snakemake-bacterial-riboseq

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

Language: Python - Size: 943 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 2 - Forks: 0

smithlabcode/riborex

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

Language: R - Size: 4.02 MB - Last synced at: about 1 month ago - Pushed at: about 4 years ago - Stars: 10 - Forks: 2

smithlabcode/ribotricer-results

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

Language: Jupyter Notebook - Size: 142 MB - Last synced at: about 1 month ago - Pushed at: over 4 years ago - Stars: 8 - Forks: 0

vam-sin/ribogl

Graph+Sequence approach to predicting ribosome densities at the gene level

Language: Python - Size: 17.6 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

xryanglab/RocA

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

Language: Python - Size: 29.8 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

ribosomeprofiling/riboflow

Pipeline for Ribosome Profiling Data

Language: Groovy - Size: 246 KB - Last synced at: about 1 year ago - Pushed at: almost 2 years ago - Stars: 13 - Forks: 9

jianhong/workshop2020

workshop2020: Basic and advanced bioinformatics for RegenerationNEXT

Language: R - Size: 129 MB - Last synced at: about 1 year ago - Pushed at: about 4 years ago - Stars: 2 - Forks: 0

Biobix/mQC

Ribosome profiling mapping quality control tool

Language: Python - Size: 260 KB - Last synced at: 6 months ago - Pushed at: about 4 years ago - Stars: 6 - Forks: 2

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: R - Size: 1.58 MB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 4

vimalkvn/riboplot 📦

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

Language: Python - Size: 2.85 MB - Last synced at: about 10 hours ago - Pushed at: almost 7 years ago - Stars: 4 - Forks: 1

sunyumail93/PipeRiboseq

A comprehensive pipeline for Ribo-seq data analysis

Language: Shell - Size: 85.4 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 10 - Forks: 1

ruggleslab/rivet

Website source code for analysis of ribosome / polysome profiling

Language: R - Size: 6.93 MB - Last synced at: 6 months ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

fallerlab/Ribo-ODDR

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

Language: Python - Size: 4.78 MB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 0

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: Python - Size: 761 KB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 13 - Forks: 4

vam-sin/rb-prof

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

Language: Python - Size: 28 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

tjh48/riboSeqR

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

Language: R - Size: 3.41 MB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

sudeepsahadevan/start_stop_analysis

Workflow for Ribosome profiling data start and stop codon analysis.

Language: Python - Size: 25.4 KB - Last synced at: almost 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 1

jvandinter/palomar-siles_et_al_2022

Language: HTML - Size: 312 KB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 1

jvandinter/container_pilot

pilot pipeline that includes tool containerization

Language: Shell - Size: 117 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

celalp/ribofootprintR

Fast data processing for ribosome footpring profiling experiments from bam files

Language: R - Size: 59.6 KB - Last synced at: 6 months ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0

saketkc/riboraptor

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

Language: Python - Size: 186 MB - Last synced at: 29 days ago - Pushed at: about 4 years ago - Stars: 13 - Forks: 0

BIONF/PhyloRBF Fork of trvinh/PhyloProfileRibi

Language: R - Size: 4.55 MB - Last synced at: 11 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

zhongyiwang1/Ribo-seq

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

Language: R - Size: 65.3 MB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 1

PSSUN/bioscript

bioinformatics scripts

Language: Python - Size: 26.4 KB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

rretkute/ML_gene_expression

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

Language: Mathematica - Size: 5.66 MB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

LewisLabUCSD/RibosomeProfiling

Analyze ribosome profiling for organisms have ncbi annotation

Language: Jupyter Notebook - Size: 511 KB - Last synced at: about 2 years ago - Pushed at: over 7 years ago - Stars: 1 - Forks: 2

saketkc/ribo-seq-snakemake

Snakemake pipeline for Ribo-Seq analysis

Language: Python - Size: 114 KB - Last synced at: about 2 months ago - Pushed at: almost 7 years ago - Stars: 2 - Forks: 0

Biobix/mQC_galaxy

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

Language: HTML - Size: 13.7 MB - Last synced at: about 2 years ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0