gtf

There are 1 repository under gtf topic.

NBISweden / AGAT
Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
agat gff perl-scripts gtf standardisation gff-format toolkit
Language:Perl 474
pyGeno
tariqdaouda / pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
bioinformatics biology genomics proteomics genome genome-annotation genome-browser genome-sequencing genomes medical medicine cancer cancer-genomics cancer-genomes ensembl gtf vcf snps csv-parser bed
Language:Python 314
genomics
igordot / genomics
A collection of scripts and notes related to genomics and bioinformatics
bioinformatics genomics sequencing illumina fasta fastq gtf vcf nanopore dna science workflow fast5
Language:R 201
sagnikbanerjee15 / Finder
A fully automated gene annotator from RNA-Seq expression data
gene-annotations rna-seq gtf finder protein-sequences changepoint-detection gene-models transcripts predict-genes bioinformatics bioinformatics-pipeline gene-annotation-pipeline genome-annotation
Language:Python 58
sbslee / fuc
Frequently used commands in bioinformatics
vcf bed fastq bioinformatics api cli bam sam cram maf visualization fasta gff gtf
Language:Python 52
dputhier / pygtftk
A python package and a set of shell commands to handle GTF files
bioinformatics gene gtf bed bigwig genomics transcript exon cds genomic tss tts splicing dna-sequences intron ngs chip-seq rna-seq
Language:Python 45
pbenner / gonetics
Go / Golang Bioinformatics Library
bigwig genomic-ranges gtf bam-files bigwig-files coverage bioinformatics bioinformatics-containers chip-seq golang golang-library
Language:Go 45
junjunlab / BioSeqUtils
Extract Sequence from Genome According to Annotation File
gtf genome transcript atac-seq chip-seq hic merip-seq coverage-plot
Language:R 31
alejandrogzi / gtfsort
a lexicographically-based GTF/GFF sorter
algorithms bioinformatics gtf sorting sorting-algorithms
Language:Rust 28
tjparnell / biotoolbox
Tools for querying and analysis of genomic data
bioinformatics bioperl bigwig bam gff3 gtf fasta chip-seq rna-seq vcf annotations
Language:Perl 27
alejandrogzi / gxf2bed
fastest GTF/GFF-to-BED converter chilling around
bed converter gene-annotation gff gtf high-performance
Language:Rust 21
dwpeng / filterx
process any file in tabular format. Fasta/fastq/GTF/GFF/VCF/SAM/BED
bioinformatics fasta fastq gff3 gtf sam tsv seqkit
Language:Rust 21
BioInterchange / Ontologies
Home of the Genomic Feature and Variation Ontology (GFVO)
ontology genomics genomic-data-science gff3 gtf gvf vcf
Language:Ruby 16
alejandrogzi / bed2gtf
high-performance BED-to-GTF converter written in Rust
bed gene-annotation genes gtf bioinformatics genome-annotation
Language:Rust 14
zyxue / gtf2csv
Convert genome annotation GTF file into plain CSV format
gtf csv genomics annotation annotation-processing gff
Language:Jupyter Notebook 14
chasewnelson / EBT
Evolutionary Bioinformatics Toolkit (EBT)
perl vcf vcf-files fasta fasta-sequences sequence sequence-alignment gtf gff dna-sequences
Language:Perl 11
reference-genomes
igordot / reference-genomes
Reference sequences and annotation files for commonly analyzed organisms
genomics genome sequencing fasta gtf annotation annotation-files
8
bioinformatist / py3_scripts
Life is short, *****.
pacbio crawler scrapy blast gtf
Language:Python 7
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.
bioinformatics rna-seq 3-rna-seq differential-expression gtf ensembl
Language:Python 6
deeptools / deeptools_intervals
A python library for constructing interval trees with associated exon/annotation information
bioinformatics interval-tree gtf bed
Language:C 6
guokai8 / gff2gene
Plot gene structure
gff3 gtf structure figure
Language:R 6
Bohdan-Khomtchouk / gtf
R package to provide gene transfer format files from commonly investigated model organisms in ChIP-seq studies
gtf chip-seq r-package bioinformatics computational-biology
Language:R 5
PoisonAlien / gtf2fasta
Tookit for gtf format conversion and sequence extraction
gtf rna-seq
Language:Julia 5
alejandrogzi / noel
GTF/GFF per gene non-overlapping exon length calculator
exon gene-annotation gff gtf length non-overlapping
Language:Rust 4
anergictcell / atg
A Rust library and CLI tool to handle genomic transcripts
bioinformatics bioinformatics-tool cli-app converter genomics gtf transcriptomics
Language:Rust 4
antonkulaga / genotations
A small library to work with ensembl and other annotations in python
bioinformatics genes genomics annotations ensembl gtf polars transcriptomics
Language:Python 3
dmyersturnbull / bioio
Micro-libraries for reading and writing genomic sequence data in various formats.
vcf bioinformatics gff3 bed fasta ucsc genome genomics gtf gvf ngs next-generation-sequencing genbank
Language:Java 3
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.
greytechno gtf mrgt
2
krooijers / gtfparser
parser gtf
Language:Python 2
mvinyard / GTFast
Lift annotations from a GTF file to an adata object.
genomics gff gtf python gencode anndata single-cell
Language:Python 2
nthomasCUBE / Gexplora
Gexplora - user-interface to analyse genomic elements along chromosomes
numpy chromosomes heatmap python tkinter stringdb oma ensembl linechart cis-element gtf annotation
Language:Python 2
biowdl / collect-columns
tsv csv rna-seq bioinformatics gtf gff
Language:Python 1
dzhang32 / tuni
Unify transcripts across different samples
gtf transcript-assembly gff
Language:Rust 1
fursham-h / factR
factR: Functional Annotation of Custom-assembled Transcripts in R
custom-transcriptomes gtf functional-annotation rna-seq-analysis
Language:R 1
jliu678 / SeqWins
An R package allowing flexible base trimming and complete Fastq analysis on Windows System
fastq-data trimming-bases feature-count gtf qc-report windows
Language:R 1
noamteyssier / gtfjson
A simple CLI utility to convert a GTF file to NDJSON for fast parsing
bioinformatics cli ensembl gtf json parsing
Language:Rust 1

gtf

NBISweden / AGAT

tariqdaouda / pyGeno

igordot / genomics

sagnikbanerjee15 / Finder

sbslee / fuc

dputhier / pygtftk

pbenner / gonetics

junjunlab / BioSeqUtils

alejandrogzi / gtfsort

tjparnell / biotoolbox

alejandrogzi / gxf2bed

dwpeng / filterx

BioInterchange / Ontologies

alejandrogzi / bed2gtf

zyxue / gtf2csv

chasewnelson / EBT

igordot / reference-genomes

bioinformatist / py3_scripts

danilotat / UTR_add_extend_GTF

deeptools / deeptools_intervals

guokai8 / gff2gene

Bohdan-Khomtchouk / gtf

PoisonAlien / gtf2fasta

alejandrogzi / noel

anergictcell / atg

antonkulaga / genotations

dmyersturnbull / bioio

GreyTechno / gtci

krooijers / gtfparser

mvinyard / GTFast

nthomasCUBE / Gexplora

biowdl / collect-columns

dzhang32 / tuni

fursham-h / factR

jliu678 / SeqWins

noamteyssier / gtfjson