jonathangoeke

uncalled4

flexiplex

The Flexible Demultiplexer

NanoporeRNASeq

Nanopore RNASeq data

squigualiser

Visualise and analyse nanopore (ONT) raw signals

f5c

Ultra-fast methylation calling and event alignment tool for nanopore sequencing data (supports CUDA acceleration)

buttery-eel

The buttery eel - a slow5 guppy/dorado basecaller wrapper

bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

nf-m6anet

A NextFlow pipeline for m6A detection from Nanopore direct RNA-seq data

awesome-nanopore

A curated list of awesome nanopore analysis tools.

cgranges

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

alternative-promoter-analysis

Alternative Promoter Analysis Packages

toil

A scalable, efficient, cross-platform (Linux/macOS) and easy-to-use workflow engine in pure Python.

MI_Workshop

A repository to host materials needed for workship in Multiple Instance Learning

bioinformatics-workflows

minimal example implementations for bioinformatics workflow managers

pychopper

A tool to identify, orient, trim and rescue full length cDNA reads

chunked

Chunkwise Text-file Processing for 'dplyr'

deSALT

deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads

m6anet

Detection of m6A from direct RNA-Seq data

deepTools

Tools to process and analyze deep sequencing data.

bioc-refcard

Bioconductor cheat sheet

common-workflow-language

Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊

Contributions

Contribute Packages to Bioconductor

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

OPERA-MS

OPERA-MS - Hybrid Metagenomic Assembler

sg-nex-data

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project

xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing

nanoseq

Nanopore demultiplexing, QC and alignment pipeline

seqan3

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

proActiv

Estimation of Promoter Activity from RNA-Seq data