NBISweden/AGAT

Another Gtf/Gff Analysis Toolkit

Language: Perl - Size: 29.2 MB - Last synced: 3 days ago - Pushed: 9 days ago - Stars: 411 - Forks: 52

danilotat/UTR_add_extend_GTF

Provided tool will add explicit 3'UTR and extends it into a valid Ensembl GTF file. It's useful for 3'RNAseq when 3' coordinates might not be as good as you expect.

Language: Python - Size: 34.2 KB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 5 - Forks: 2

alejandrogzi/gtfsort

A chr/pos/feature GTF sorter that uses a lexicographically-based index ordering algorithm.

Language: Rust - Size: 619 KB - Last synced: 6 days ago - Pushed: 2 months ago - Stars: 24 - Forks: 1

tjparnell/biotoolbox

Tools for querying and analysis of genomic data

Language: Perl - Size: 7.34 MB - Last synced: 20 days ago - Pushed: 20 days ago - Stars: 27 - Forks: 16

anergictcell/atg

A Rust library and CLI tool to handle genomic transcripts

Language: Rust - Size: 437 KB - Last synced: 18 days ago - Pushed: 22 days ago - Stars: 4 - Forks: 0

alejandrogzi/gxf2bed

Fastest GTF/GFF-to-BED converter chilling around

Language: Rust - Size: 188 KB - Last synced: 13 days ago - Pushed: about 2 months ago - Stars: 14 - Forks: 0

tariqdaouda/pyGeno

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

Language: Python - Size: 10.6 MB - Last synced: 23 days ago - Pushed: 7 months ago - Stars: 307 - Forks: 52

dputhier/pygtftk

A python package and a set of shell commands to handle GTF files

Language: Python - Size: 143 MB - Last synced: 7 days ago - Pushed: 5 months ago - Stars: 42 - Forks: 6

BioInterchange/Ontologies

Home of the Genomic Feature and Variation Ontology (GFVO)

Language: Ruby - Size: 738 KB - Last synced: about 2 months ago - Pushed: about 3 years ago - Stars: 16 - Forks: 4

alejandrogzi/bed2gtf

A high-performance BED-to-GTF converter written in Rust

Language: Rust - Size: 145 KB - Last synced: 29 days ago - Pushed: 29 days ago - Stars: 8 - Forks: 0

sbslee/fuc

Frequently used commands in bioinformatics

Language: Python - Size: 1.17 MB - Last synced: 9 days ago - Pushed: 8 months ago - Stars: 44 - Forks: 5

fabbio00/GTF-to-Protein-FASTA-Converter

This project consists of a Python script designed to convert coding sequences found in a GTF (Gene Transfer Format) file to protein sequences in the FASTA format. The code was developed as part of a university project for genomic sequence analysis.

Language: Jupyter Notebook - Size: 896 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

deeptools/deeptools_intervals

A python library for constructing interval trees with associated exon/annotation information

Language: C - Size: 260 KB - Last synced: 21 days ago - Pushed: almost 5 years ago - Stars: 6 - Forks: 2

pbenner/gonetics

Go / Golang Bioinformatics Library

Language: Go - Size: 6.08 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 37 - Forks: 1

nRo/DataFrame-GTF

GTF parser for Java Dataframes

Language: Java - Size: 26.4 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 1

PoisonAlien/gtf2fasta

Tookit for gtf format conversion and sequence extraction

Language: Julia - Size: 10.7 KB - Last synced: 2 days ago - Pushed: 4 months ago - Stars: 5 - Forks: 1

dmyersturnbull/bioio Fork of PharmGKB/genome-sequence-io

Micro-libraries for reading and writing genomic sequence data in various formats.

Language: Java - Size: 690 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 3 - Forks: 0

igordot/genomics

A collection of scripts and notes related to genomics and bioinformatics

Language: R - Size: 241 KB - Last synced: 3 months ago - Pushed: over 1 year ago - Stars: 182 - Forks: 51

antonkulaga/genotations

A small library to work with ensembl and other annotations in python

Language: Python - Size: 3.65 MB - Last synced: 3 days ago - Pushed: 8 months ago - Stars: 2 - Forks: 0

alejandrogzi/noel

GTF/GFF per gene non-overlapping exon length calculator

Language: Rust - Size: 734 KB - Last synced: 8 days ago - Pushed: 4 months ago - Stars: 3 - Forks: 0

GreyTechno/gtci

An installer for GTF (command line installer) simplifies software installation & dependency management for developers, beginners, and admins. It's a quick & automated way to install software, making it an essential tool in any deployment or dev pipeline, particularly for automating the installation process and avoiding delays.

Size: 33.2 KB - Last synced: 1 day ago - Pushed: 5 months ago - Stars: 2 - Forks: 0

Puriney/MrY

Management of References for Yourself

Language: Python - Size: 69.3 KB - Last synced: 7 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

bingbig/gtf2gff3

Convert gtf to gff3 for JBrowse

Language: Python - Size: 2.93 KB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 1

nthomasCUBE/Gexplora

Gexplora - user-interface to analyse genomic elements along chromosomes

Language: Python - Size: 43.7 MB - Last synced: 7 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0

sagnikbanerjee15/Finder

A fully automated gene annotator from RNA-Seq expression data

Language: Python - Size: 247 MB - Last synced: 7 months ago - Pushed: 11 months ago - Stars: 50 - Forks: 14

junjunlab/BioSeqUtils

Extract Sequence from Genome According to Annotation File

Language: R - Size: 967 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 21 - Forks: 0

cumbof/OpenGDC

An open-source Java tool to automatically extract and convert all clinical and genomic data from the Genomic Data Commons to BED, GTF, CSV, and JSON format

Language: Java - Size: 237 MB - Last synced: 8 months ago - Pushed: about 3 years ago - Stars: 0 - Forks: 1

willeccles/gtf-cpp

Header-only C++ GTF file parser.

Language: C++ - Size: 39.1 KB - Last synced: 5 months ago - Pushed: over 4 years ago - Stars: 3 - Forks: 1

ohdongha/Genome-Toolbox

Custom python scripts useful for working with genome assemblies and annotations

Language: Python - Size: 64.5 KB - Last synced: 9 months ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

noamteyssier/gtfjson

A simple CLI utility to convert a GTF file to NDJSON for fast parsing

Language: Rust - Size: 70.3 KB - Last synced: 11 days ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

sivkri/exon-bed-generator

Exon BED Generator: A script to download, process, and generate a BED file with exon coordinates for Homo sapiens from a GTF file

Language: Shell - Size: 1000 Bytes - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

sivkri/gene-info-extractor

Gene Info Extractor: A Python script to extract gene information and annotations from CSV data

Language: Python - Size: 46.9 KB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

sivkri/extract-information-from-gtf

To filter and extract information based on your required input

Language: Python - Size: 2.71 MB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

zyxue/gtf2csv

Convert genome annotation GTF file into plain CSV format

Language: Jupyter Notebook - Size: 1.57 MB - Last synced: about 1 year ago - Pushed: over 5 years ago - Stars: 12 - Forks: 2

fursham-h/factR

factR: Functional Annotation of Custom-assembled Transcripts in R

Language: R - Size: 12.6 MB - Last synced: 19 days ago - Pushed: 9 months ago - Stars: 1 - Forks: 0

chasewnelson/EBT

Evolutionary Bioinformatics Toolkit (EBT)

Language: Perl - Size: 99.6 KB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 10 - Forks: 4

jacobbierstedt/gfftobed

Convert GFF3/GTF to BED

Language: C++ - Size: 55.7 KB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 5 - Forks: 2

guokai8/gff2gene

Plot gene structure

Language: R - Size: 37.1 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 4 - Forks: 0

Bohdan-Khomtchouk/gtf

R package to provide gene transfer format files from commonly investigated model organisms in ChIP-seq studies

Language: R - Size: 88.5 MB - Last synced: about 1 year ago - Pushed: almost 7 years ago - Stars: 5 - Forks: 0

mvinyard/GTFast

Lift annotations from a GTF file to an adata object.

Language: Python - Size: 48.8 KB - Last synced: 1 day ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 0

igordot/reference-genomes

Reference sequences and annotation files for commonly analyzed organisms

Size: 27.6 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 3 - Forks: 4

bioinformatist/py3_scripts

Life is short, *****.

Language: Python - Size: 28.3 KB - Last synced: about 1 year ago - Pushed: over 7 years ago - Stars: 7 - Forks: 3

jliu678/SeqWins

An R package allowing flexible base trimming and complete Fastq analysis on Windows System

Language: R - Size: 112 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 1 - Forks: 0

biowdl/collect-columns

Language: Python - Size: 46.9 KB - Last synced: 29 days ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

krooijers/gtfparser

Language: Python - Size: 2.93 KB - Last synced: 11 months ago - Pushed: over 6 years ago - Stars: 2 - Forks: 0

biopet/addgenesandtranscriptstogtf

Language: Scala - Size: 353 KB - Last synced: 11 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

seandavi/RNASeqBeginnerTutorial

An introduction to RNA-seq file formats, quality control, and visualization targeted to a biologist audience

Size: 5.89 MB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 1 - Forks: 2