cihanerkut

JAFFA

JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusions

LongGF

A computational algorithm and software tool for fast and accurate detection of gene fusion by long-read transcriptome sequencing

useful-sed

Useful sed scripts & patterns.

arriba

Fast and accurate gene fusion detection from RNA-Seq data

bambu

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

drawCell

R package to create cell pictures.

modern-unix

A collection of modern/faster/saner alternatives to common unix commands.

m6anet

Detection of m6A from direct RNA-Seq data

nanoseq

Nanopore demultiplexing, QC and alignment pipeline

deeplexicon

Signal based nanopore RNA demultiplexing with convolutional neural networks

iptv

Collection of publicly available IPTV channels from all over the world

nanom6A

xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing

EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)

NA12878

Data and analysis for NA12878 genome on nanopore

mice

Multivariate Imputation by Chained Equations

nanocompore

RNA modifications detection from Nanopore dRNA-Seq data

ganttrify

Create beautiful Gantt charts with ggplot2

awesome-bioinformatics-benchmarks

A curated list of bioinformatics bench-marking papers and resources.

ViewPipeSteps

Create tabs of View() output for each chained pipe

seqkit

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

iheatmapr

Complex, interactive heatmaps in R

defmacro

Load Time R Package Macros

flair

Full-Length Alternative Isoform analysis of RNA

megalodon

Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.

pomoxis

Analysis components from Oxford Nanopore Research

vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

doc-ANNOVAR

Documentation for the ANNOVAR software

cowplot

cowplot: Streamlined Plot Theme and Plot Annotations for ggplot2

isovar

Assembly of RNA reads to determine the effect of a cancer mutation on protein sequence