Edinburgh-Genome-Foundry/python_codon_tables

:bar_chart: Codon usage tables in code-friendly format + Python bindings

Language: Python - Size: 66.4 KB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 37 - Forks: 11

Koeng101/dnadesign

A Go package for designing DNA.

Language: Go - Size: 36.8 MB - Last synced at: about 1 month ago - Pushed at: 5 months ago - Stars: 30 - Forks: 1

SouradiptoC/CodonU

A python project for analysis of codon usage for gene or genome analysis

Language: Python - Size: 64.4 MB - Last synced at: about 1 month ago - Pushed at: 6 months ago - Stars: 21 - Forks: 1

alondmnt/codon-bias

Python package of codon usage bias analysis tools

Language: Python - Size: 203 KB - Last synced at: 5 days ago - Pushed at: 2 months ago - Stars: 16 - Forks: 7

IQTLabs/freqgen 📦

🎯 Generate DNA sequences with specified amino acid, codon, and k-mer frequencies

Language: Python - Size: 2.45 MB - Last synced at: 2 months ago - Pushed at: over 2 years ago - Stars: 16 - Forks: 4

rhondene/Codon-Usage-in-Python

My Python3 package to compute common codon usage statistics given a FASTA of DNA sequences

Language: Python - Size: 815 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 12 - Forks: 1

Kalan-Lab/codoff

codoff: a program to measure the irregularity of the codon usage for a single genomic region (e.g. a BGC, phage, etc.) relative to the full genome.

Language: Python - Size: 3.82 MB - Last synced at: 9 days ago - Pushed at: about 1 month ago - Stars: 11 - Forks: 1

smsaladi/codonw-slim

A slimmed down fork of CodonW with python bindings

Language: C - Size: 2.04 MB - Last synced at: 8 months ago - Pushed at: about 2 years ago - Stars: 7 - Forks: 6

tdseher/simple-codon-optimizer

Simple Python program to perform codon optimization or heterology calculations.

Language: Python - Size: 31.3 KB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 7 - Forks: 2

mt1022/cubar

R Package for Codon Usage Bias Analysis

Language: R - Size: 19.3 MB - Last synced at: 11 days ago - Pushed at: 5 months ago - Stars: 6 - Forks: 2

alondmnt/codon-usage

MATLAB package for codon usage bias and NGS analysis

Language: MATLAB - Size: 40 KB - Last synced at: 5 days ago - Pushed at: about 2 years ago - Stars: 5 - Forks: 1

gxelab/cubat 📦

Currently, we don't have the bandwidth to update and maintain the Python version; please use the R version instead. (https://github.com/mt1022/cubar)

Language: Python - Size: 14.5 MB - Last synced at: 3 days ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 2

lindechun/CodonM

Comparative analysis pipeline of Population's Codon Usage

Language: Python - Size: 1.47 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 4 - Forks: 0

smsaladi/codonpair

A codon pair score/codon pair bias calculator

Language: Perl - Size: 846 KB - Last synced at: 10 months ago - Pushed at: about 5 years ago - Stars: 4 - Forks: 3

juanvillada/CodG

Analysis of codon positional dependency

Language: R - Size: 211 MB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 3 - Forks: 0

ostash-group/GeneticPlotter

A tool with nice GUI to visualize the codon usage frequencies in whole genomes

Language: Python - Size: 1.82 MB - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 3 - Forks: 1

Bohdan-Khomtchouk/Gaussian-distributed-codon-frequencies-of-genomes

Source code to accompany manuscript entitled "Gaussian-distributed codon frequencies of genomes" (Khomtchouk & Nonner, 2019)

Language: D - Size: 65.4 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 3 - Forks: 0

stracquadaniolab/cubseq-nf

CUBseq analyses codon usage bias from RNA-seq data, producing robust CUB estimates that account for variants transcriptome-wide and in highly expressed genes.

Language: R - Size: 187 MB - Last synced at: about 2 months ago - Pushed at: about 1 year ago - Stars: 2 - Forks: 1

Gumgo91/CodonHumanization

A Novel Approach to Codon Optimization Based on Machine Learning and Genetic Algorithm

Language: Jupyter Notebook - Size: 32.6 MB - Last synced at: 8 months ago - Pushed at: about 2 years ago - Stars: 2 - Forks: 1

dyyvgug/CUBE

Calculate CUB indices and optimize the gene sequence to enhance expression

Language: Roff - Size: 37.5 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 1 - Forks: 0

anchitaaghag/Codon-Optimization-for-Biopharming

A tool to translate a given protein sequence into a DNA sequence based on a constructed codon use table for a target heterologous host, Nicotiana benthamiana.

Language: R - Size: 2.08 MB - Last synced at: about 1 year ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

chaupka/codon_harmonization

A script for codon harmonization.

Language: Python - Size: 19.5 KB - Last synced at: about 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

webermarcolivier/codon_usage_oncogenes

Analysis of codon usage in oncogene families.

Language: Jupyter Notebook - Size: 1.92 MB - Last synced at: 10 months ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

BrianDehlinger/DCB-Dynamic-Codon-Biaser

A tool for dynamically calculating the codon usage bias in bacterial genomes and querying of a database for Codon Bias statistical analysis

Language: Python - Size: 64.3 MB - Last synced at: 8 months ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

bibymaths/codonanalyzer

A collection of Perl scripts for analyzing DNA and protein sequences, featuring tools for rare codon detection, GC content profiling, and hydropathy plotting, optimized for Escherichia coli datasets.

Language: Perl - Size: 16.1 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

Mordziarz/RSCUcaller

Program in R for calculating RSCU.

Language: R - Size: 6.08 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 0

Samia35-2973/Living-Type-Classification-from-Codon-Usage

Machine learning project to classify living types based on codon usage data using Random Forest and XGBoost classifiers.

Language: Jupyter Notebook - Size: 8.73 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

GabrielFalque/codon_ugene

Compute and produce results about codon usage in a genome CDS.

Language: R - Size: 57.6 KB - Last synced at: 3 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

dominiquefastus/NuStru-CodonAnalysis

Retrieving nucleotide sequences for PDB and Uniprot structure on a large scale. Analysis of synonymous codons and codon usage on protein structure and evolution.

Language: Jupyter Notebook - Size: 3.87 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0

Lennart2001/codon-usage

Predicting Taxonomic Identity and Genetic Composition of Codon Usage Bias Levels Using Deep Learning Models

Language: TeX - Size: 18 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

MPurushothamRao/Codon-Optimiser-by-codon-bias

It is simple codon optimiser by using codon bias and usage

Language: Python - Size: 107 KB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

mariachiaragrieco/TIPre

Taxonomic Identity PREdiction: homework for Machine Learning Course 2021 (MSc Bioinformatics for Computational Genomics)

Language: Jupyter Notebook - Size: 6.29 MB - Last synced at: about 1 year ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

dzhang32/codino

Calculating AA frequencies from codon design, and vice versa

Language: Python - Size: 2.91 MB - Last synced at: 25 days ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

juanvillada/H_bonds_ramp

Research on position-dependent hydrogen bonds per codon

Language: R - Size: 42.9 MB - Last synced at: over 1 year ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 3

samdarshihawk/Codon-decoder

Codon decoder, taking a input from user, then the program will display the type protein created by the codon

Language: Java - Size: 1000 Bytes - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

kyu999/codon_usage_chart

Language: JavaScript - Size: 133 KB - Last synced at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0