Git Product home page Git Product logo

felixgrunberger / microbepore Goto Github PK

View Code? Open in Web Editor NEW
5.0 5.0 1.0 16.5 MB

This is the repository for the manuscript “Expanding the transcriptomic toolbox in prokaryotes by Nanopore sequencing of RNA and cDNA molecules.” In this study, we applied and benchmarked all currently available RNA-seq kits from Oxford Nanopore technologies to analyse RNAs in the prokaryotic model organism Escherichia coli K-12.

Home Page: https://felixgrunberger.github.io/microbepore

License: MIT License

R 100.00%
nanopore-sequencing

microbepore's Introduction

  • 👋 Hi, I’m @felixgrunberger
  • 👀 I’m interested in Microbiology 🦠, Transcriptomics, Sequencing, Data analysis 💻, Data visualization 📊 (in R) and many more things
  • 🌱 I’m currently learning how to use Nanopore RNA-seq data to expand the transcriptomic toolbox in prokaryotes ✌️
  • 📫 Contact me on twitter

microbepore's People

Contributors

felixgrunberger avatar

Stargazers

avatar avatar avatar avatar avatar

Watchers

avatar avatar

Forkers

zubeirelahmad

microbepore's Issues

ModuleNotFoundError: No module named 'idr' : termseq-peaks

Hi Felix,
Got an error while ran the script for calling the peaks.

$ termseq_peaks /media/majorram/Analysis_Data/singhrn/transcriptome_atlas/tss/trimmed/output/barcode07.plus.bedgraph /media/majorram/Analysis_Data/singhrn/transcriptome_atlas/tss/trimmed/output/barcode08.plus.bedgraph /media/majorram/Analysis_Data/singhrn/transcriptome_atlas/tss/trimmed/output/barcode09.plus.bedgraph --peaks /media/majorram/Analysis_Data/singhrn/transcriptome_atlas/tss/trimmed/output/barcode789.plus.peaks --strand +
Traceback (most recent call last):
File "/home/majorram/anaconda3/bin/termseq_peaks", line 11, in
from peaklib.peaklib import idr_peak_calls
File "/home/majorram/anaconda3/lib/python3.9/site-packages/peaklib/peaklib.py", line 6, in
from idr import idr
ModuleNotFoundError: No module named 'idr'

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.