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bioinformatics-notes.github.io

deepmod

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications

epinano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads

flair

Full-Length Alternative Isoform analysis of RNA

flypig

make code fly

hemtools

HemTools: a collection of NGS pipelines and bioinformatic analyses

hic_tools

A collection of tools for Hi-C data analysis

hichip

HiChiP QC and data analysis

hichipper

A preprocessing and QC pipeline for HiChIP data

hicplotter

“When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau

imap

A novel unsupervised batch removal framework, called iMAP, based on neural networks.

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

model_search

mybook

nano-cop

Nanopore analysis of CO-transcriptional processing exposes the nascent transcriptome via direct long-read RNA-seq

nanom6a

polya_analysis

Analysis pipeline of poly(A) tails lengths from ONT poly(A) standards dataset. Accompanies our forthcoming publication.

scisa-tools

single-cell-Isoform-Sequencing-Analysis-Tools: New and powerful tools brings single-cell RNA sequencing to the Isoform level and single molecule resolution.

scrnaseq_pipelines

star

RNA-seq aligner

umi-tools

Tools for handling Unique Molecular Identifiers in NGS data sets