Extract gene length based on featureCount calculation gene nonredundant exon length method.

Last update: Nov 21, 2022

Related tags

Overview

GetGeneLength Package

Extract gene length based on featureCount calculation gene nonredundant exon length method.
If you want to calculate TPM/FPKM/RPKM to visualize results and for other downstream analysis with only count matrix, you can use this GetGeneLength function to get gene length information and get normalized values.

Install

$ pip install GetGeneLength

# for lattest version
$ pip install GetGeneLength==0.0.3

Usage

help infomation:

$ GetGeneLength -h
usage: GetGeneLength --database ensembl --gtffile gencode.v38.annotation_human.gtf --lengthfile gene_length.txt

Get gene length from GTF annotation file.

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit
  -d {ucsc,ensembl,gencode}, --database {ucsc,ensembl,gencode}
                        which annotation database you choose. (default="ensembl")
  -g GTFFILE, --gtffile GTFFILE
                        input your GTF file. (ucsc/ensembl/gencode)
  -l LENGTH_INFO, --lengthfile LENGTH_INFO
                        output your gene lenth file. (gene_length.txt)

Thank your for your support, if you have any questions or suggestions please contact me: [email protected].

for ucsc gtf file:

$ GetGeneLength -d ucsc -g hg38.ncbiRefSeq.gtf -l ucsc_gene_length.txt
Your job is running, please wait...

Your job is done!

$ head -n 3 ucsc_gene_length.txt
TRNP	TRNP	68
TRNT	TRNT	66
CYTB	CYTB	1141

for gencode/ensembl gtf file:

$ GetGeneLength -d gencode -g gencode.v38.annotation_human.gtf -l gene_length.txt
Your job is running, please wait...

Your job is done!

$ head -n 3 gene_length.txt
DDX11L1	ENSG00000223972.5	transcribed_unprocessed_pseudogene	1735
WASH7P	ENSG00000227232.5	unprocessed_pseudogene	1351
MIR6859-1	ENSG00000278267.1	miRNA	68

A little tool that uses LLVM to extract simple "what does this do" level instruction information from all architectures.

moirai: MOre InstRuctions and Information Backcronym. Anyway, this is a small project to extract useful instruction definitions from LLVM's platform d

2 Jul 30, 2022

「📖」Tool created to extract metadata from a domain

Metafind is an OSINT tool created with the aim of automating the search for metadata of a particular domain from the search engine known as Google.

9 Dec 28, 2022

JD-backup is an advanced Python script, that will extract all links from a jDownloader 2 file list and export them to a text file.

3 Jun 7, 2022

$Implementation of the Angular Spectrum method in Python to simulate Diffraction Patterns$

Implementation of the Angular Spectrum method in Python to simulate Diffraction Patterns

Diffraction Simulations - Angular Spectrum Method Implementation of the Angular Spectrum method in Python to simulate Diffraction Patterns with arbitr

276 Dec 30, 2022

Python implementation of the ASFLIP advection method

This is a python implementation of the ASFLIP advection method . We would like to hear from you if you appreciate this work.

133 Nov 13, 2022

This is a method to build your own qgis configuration packages using osgeo4W.

This is a method to build your own qgis configuration packages using osgeo4W. Then you can automate deployment in your organization with a controled and trusted environnement.

26 Dec 5, 2022

tetrados is a tool to generate a density of states using the linear tetrahedron method from a band structure.

tetrados tetrados is a tool to generate a density of states using the linear tetrahedron method from a band structure. Currently, only VASP calculatio

1 Dec 21, 2021

Implementation of the MDMC method to search for magnetic ground state using VASP

Implementation of MDMC method ( by Olga Vekilova ) to search for magnetic ground state using VASP

1 Nov 27, 2021

A simple method to create strong password.

1 Jan 23, 2022

Extract gene length based on featureCount calculation gene nonredundant exon length method.

Related tags

Overview

GetGeneLength Package

Install

Usage

You might also like...

A little tool that uses LLVM to extract simple "what does this do" level instruction information from all architectures.

「📖」Tool created to extract metadata from a domain

JD-backup is an advanced Python script, that will extract all links from a jDownloader 2 file list and export them to a text file.

Implementation of the Angular Spectrum method in Python to simulate Diffraction Patterns

Python implementation of the ASFLIP advection method

This is a method to build your own qgis configuration packages using osgeo4W.

tetrados is a tool to generate a density of states using the linear tetrahedron method from a band structure.

Implementation of the MDMC method to search for magnetic ground state using VASP

A simple method to create strong password.

Releases(GetGeneLength_V0.0.3)

GetGeneLength_V0.0.3(Jan 21, 2022)

Owner

laojunjun

Rufus port to linux, writed on Python3

BestBuy Script Designed to purchase any item when it becomes available.

py-js: python3 objects for max

For my Philips Airpurifier AC3259/10

basic tool for NFT. let's spam, this is the easiest way to generate a hell lotta image

Absolute solvation free energy calculations with OpenFF and OpenMM

A compiler for ARM, X86, MSP430, xtensa and more implemented in pure Python

Oregon State University grade distributions from Fall 2018 through Summer 2021

200 LeetCode problems

A complex language with high level programming and moderate syntax.

Astroquery is an astropy affiliated package that contains a collection of tools to access online Astronomical data.

Python Multilingual Ucrel Semantic Analysis System

GitHub Actions Version Updater Updates All GitHub Action Versions in a Repository and Creates a Pull Request with the Changes.

take home quiz

Earth centric orbit propagation tool. Built from scratch in python.

IST-Website - IST Tutoring Portal for python

Python script to combine the statistical results of a TOPAS simulation that was split up into multiple batches.

Academic planner application designed for students and counselors.

Pygments is a generic syntax highlighter written in Python

Nesse repositório serão armazenados os conteúdos de aula