unique379r

strspy

STRspy: a novel alignment and quantification-based state-of-the-art method, short tandem repeat (STR) detection calling tool designed specifically for long-read sequencing reads such as from Oxford nanopore technology (ONT) and PacBio.

AGAT

Another Gtf/Gff Analysis Toolkit

arriba

Fast and accurate gene fusion detection from RNA-Seq data

automate-cv-rmd

Automate your CV - easy as 1, 2, knit! A workshop to get from data to professional CV using R Markdown presented at R-Ladies Melbourne

bedqc

BED QC tool (in the making)

bioinfo-scripts

General purpose scripts

brownbear-isoseq-act-hib

Code for Long-read isoform sequencing reveals tissue-specific isoform expression between active and hibernating brown bears (Ursus arctos)

cbs-mirseq

CBS-miRSeq: a robust comprehensive bioinformatics pipeline for microRNA expression profiling by next generation sequencing.

cDNA_Cupcake

Miscellaneous collection of Python and R scripts for processing Iso-Seq data

FixItFelix

FuSViz

A web app to visualise, interpret and prioritise genomic/transcriptomic structural variations (SVs) of multiple samples.

GeneVar2

getSequenceInfo

A Perl script allowing to get sequence information from GenBank, RefSeq or ENA sequence repositories

ggtranscript

Visualizing transcript structure and annotation using ggplot2

intervene

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets

isoseq

Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.

levioSAM

Lift-over alignments from variant-aware references

Liftoff

An accurate GFF3/GTF lift over pipeline

LIQA

Long-read Isoform Quantification and Analysis

pkg-building

python-data-visualization

Python Data Visualization course code and examples

RNA-Seq_analysis

scripts for RNA-Seq analysis

RNAseq2func

A comprehensive RNA analysis from sequence to function and pathway reporting

rnaxsv

seq2func

A comprehensive RNA analysis from sequence to function and pathway reporting

snakemake-wrappers

:snake: Snakemake wrappers for bioinformatics.

straglr

svxplorer

T2T-CHM13-hub

Assembly hub for T2T CHRM13 assemblies

YouTubeTutorials