NAL-i5K/GFF3toolkit

Python programs for processing GFF3 files

Language: Python - Size: 31.9 MB - Last synced: about 7 hours ago - Pushed: about 1 month ago - Stars: 86 - Forks: 26

NBISweden/AGAT

Another Gtf/Gff Analysis Toolkit

Language: Perl - Size: 29.2 MB - Last synced: 2 days ago - Pushed: 9 days ago - Stars: 411 - Forks: 52

chrovis/cljam

A DNA Sequence Alignment/Map (SAM) library for Clojure

Language: Clojure - Size: 35.1 MB - Last synced: 18 days ago - Pushed: 18 days ago - Stars: 88 - Forks: 12

SouthGreenPlatform/AgroLD_ETL

AgroLD is a RDF knowledge base that consists of data integrated from a variety of plant resources and ontologies. AgroLD ETL is the Python packages developed to transform plant datasets in RDF. Packages are developped for data standards such as GFF,GAF, VCF and specific plant databases.

Language: Python - Size: 1.81 MB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 1 - Forks: 1

moshi4/pyGenomeViz

A genome visualization python package for comparative genomics

Language: Python - Size: 47.8 MB - Last synced: 25 days ago - Pushed: 7 months ago - Stars: 227 - Forks: 20

alejandrogzi/gxf2bed

Fastest GTF/GFF-to-BED converter chilling around

Language: Rust - Size: 188 KB - Last synced: 13 days ago - Pushed: about 1 month ago - Stars: 14 - Forks: 0

NickJD/StORF-Reporter

Package to extract Unannotated Regions from prokaryotic genomes report coding and pseudogenised genes delimited by stop codons - Named StORFs (Stop - Open Reading Frames)

Language: Python - Size: 222 MB - Last synced: 10 days ago - Pushed: 2 months ago - Stars: 15 - Forks: 1

biodatamodels/gff-schema

LinkML schema for GFF3, the Genome Feature Format

Language: Python - Size: 5.2 MB - Last synced: 3 days ago - Pushed: over 2 years ago - Stars: 6 - Forks: 0

wurmlab/flo

Same species annotation lift over pipeline.

Language: Ruby - Size: 4.45 MB - Last synced: about 2 months ago - Pushed: 10 months ago - Stars: 89 - Forks: 28

candYgene/siga

Semantically Interoperable Genome Annotations

Language: Python - Size: 8.21 MB - Last synced: about 2 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 2

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

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

miRTop/mirtop

command lines tool to annotate miRNAs with a standard mirna/isomir naming

Language: Python - Size: 1.53 MB - Last synced: 21 days ago - Pushed: about 2 years ago - Stars: 18 - Forks: 20

scbirlab/bioino

💻 Interconverting FASTA, GFF, and CSV.

Language: Python - Size: 1.81 MB - Last synced: 21 days ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

alejandrogzi/noel

GTF/GFF per gene non-overlapping exon length calculator

Language: Rust - Size: 734 KB - Last synced: 7 days ago - Pushed: 4 months ago - Stars: 3 - Forks: 0

drozdovapb/myBedGtfGffVcfTools

home-made scripts to manipulate sequence annotation file formats (gff / vcf / genbank)

Language: Python - Size: 2.89 MB - Last synced: 5 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 1

LBGC-CFB/SpliceLauncher

RNAseq pipeline for alternative splicing junctions

Language: R - Size: 35 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 9 - Forks: 8

findell666/nwn-3t-items

A python code to display Player Character (PC) items from a NWN BIC file, in a human friendly form. This is meant to be used with ThreeTowns server items (custom 2da files)

Language: Python - Size: 7.25 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 3 - Forks: 0

wrf/genomeGTFtools

convert various features into a GFF-like file for use in genome browsers

Language: Python - Size: 3.8 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 52 - Forks: 25

ginkgobioworks/edge

Efficiently keep track of changes to genomes

Language: Python - Size: 37.6 MB - Last synced: 29 days ago - Pushed: 3 months ago - Stars: 38 - Forks: 4

tdseher/addtag-project

CRISPR/Cas-directed HDR genome editing suite: finds+scores gRNA targets, generates donor DNAs, & produces optimal cPCR primer designs.

Language: Python - Size: 2.67 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 7 - Forks: 2

biomadeira/BioDownloader

📦 A Command Line Tool for downloading protein structures, sequences and MSAs

Language: Python - Size: 47.9 KB - Last synced: 7 months ago - Pushed: over 6 years ago - Stars: 9 - Forks: 0

raymondkiu/16S_extraction_Barrnap

Automated 16S sequence extraction using Barrnap output gff files

Language: Shell - Size: 3.91 KB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 1

zglu/ModifyApolloGFF

Modify the gff export from Apollo, changing Name to ID.

Language: Python - Size: 8.79 KB - Last synced: 7 months ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

baoxingsong/GEAN

This toolkit deals with GEnomic sequence and genome structure ANnotation files between inbreeding lines and species.

Language: C++ - Size: 108 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 38 - Forks: 8

ProgrammingLife2017/DynamiteAndButterflies

Genome parser and visualisation

Language: Java - Size: 7.92 MB - Last synced: 9 months ago - Pushed: over 1 year ago - Stars: 3 - Forks: 1

fmalmeida/gff-toolbox

Gff-toolbox is a toolbox of commands that enables one to get the gist of their GFF annotation files, as well as to analyse them in different ways.

Language: Python - Size: 77.9 MB - Last synced: 9 months ago - Pushed: about 1 year ago - Stars: 6 - Forks: 1

aniketk21/tfbs-prediction

Predicting Transcription Factor Binding Sites from ENCODE data using Machine Learning

Language: Python - Size: 6.32 MB - Last synced: 9 months ago - Pushed: almost 7 years ago - Stars: 2 - Forks: 0

mcamagna/GFF2DDBJ

This tool will convert GFF3 files into DDBJ annotation files. It was created to work with Braker2 generated GFF files, but should work with any other GFF3 file as well.

Language: Python - Size: 341 KB - Last synced: 10 months ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

CromFr/nwn-lib-d

Library & tools for handling Neverwinter Nights 1/2 resources files

Language: D - Size: 36.1 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 7 - Forks: 1

YoannPa/Gff3ToBed

Language: Shell - Size: 22.5 KB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 4 - Forks: 3

bpucker/RNA-Seq_analysis

scripts for RNA-Seq analysis

Language: Python - Size: 89.8 KB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 16 - Forks: 8

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

telatin/bamtocov

🏔 coverage extraction from BAM/CRAM files, supporting targets 📊  

Language: Nim - Size: 33.1 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 45 - Forks: 4

acsamson/ImageFusion-Algorithm

ImageFusion algorithm, SSIM and PSNR evaluation（常见图像融合算法以及SSIM和PSNR评价

Language: MATLAB - Size: 76.5 MB - Last synced: 11 months ago - Pushed: over 2 years ago - Stars: 8 - 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

NAL-i5K/AgBioData_GFF3_recommendation

The AgBioData GFF3 working group has developed recommendations to solve common problems in the GFF3 format. We suggest improvements for each of the GFF3 fields, as well as the special cases of modeling functional annotations, and standard protein-coding genes. We welcome discussion of these recommendations from the larger community.

Size: 573 KB - Last synced: 28 days ago - Pushed: over 2 years ago - Stars: 5 - Forks: 4

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

milesroberts-123/extract-promoter-sequences

Extract sequences upstream of genes in a fasta file based on coordinates listed in a gff file.

Language: Shell - Size: 30.3 KB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 5 - Forks: 2

Mingun/serde-gff

Реализация формата Bioware GFF для Rust

Language: Rust - Size: 88.9 KB - Last synced: about 19 hours ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

NCBI-Hackathons/Master_gff3_parser

Convert sequence IDs between ucsc/refseq/genbank

Language: Python - Size: 1.12 MB - Last synced: 10 days ago - Pushed: over 5 years ago - Stars: 16 - Forks: 5

biowdl/collect-columns

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

milesroberts-123/extract-annotations

Use Biopython to extract functional gene annotations from a GFF file and output them as a tab-delimited text file.

Language: Python - Size: 3.54 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

NLeSC/candYgene

Language: Python - Size: 8.18 MB - Last synced: 25 days ago - Pushed: almost 7 years ago - Stars: 2 - Forks: 0

corwur/gfftoneo4j

Tools for importing GFF files to a Neo4J graph database

Language: Scala - Size: 6.67 MB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 2 - Forks: 0

bmle/G4Pipeline

A pipeline for reporting information on G-quadruplexes relative to coding regions and non-aligned regions.

Language: Python - Size: 44.9 KB - Last synced: about 1 year ago - Pushed: over 6 years ago - Stars: 1 - Forks: 0