Oshlack

splatter

Simple simulation of single-cell RNA sequencing data

JAFFA

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

Corset

Software for clustering de novo assembled transcripts and counting overlapping reads

Lace

Building SuperTranscripts: A linear representation of transcriptome data

STRetch

Method for detecting STR expansions from short-read sequencing data

Clinker

Gene Fusion Visualiser

speckle

R package for specialised analysis of single cell data

MINTIE

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

necklace

Combine reference and assembled transcriptomes for RNA-Seq analysis

Slinker

Slinker offers a succinct and complementary method to visualise RNA-Seq data through superTranscripts.

ALLSorts

ALLSorts is a B-Cell Acute Lymphoblastic Leukemia (B-ALL) subtype classifier. From gene expression counts to over 18 subtypes.

missMethyl

Bioconductor package for analysis of methylation data from Illumina's Infinium HumanMethylation arrays.

combes-organoid-paper

Analysis code and output for the Combes kidney organoid scRNA-seq paper https://doi.org/10.1186/s13073-019-0615-0

methyl-geneset-testing

ec-dtu-pipe

Pipeline for performing differential transcript usage analysis using equivalence classes, transcript quantifications and/or exon counts

hashtag-demux-paper

Analysis code for "Benchmarking single-cell hashtag oligo demultiplexing methods" paper

Toblerone

ALL-RNAseq-utility-paper

OrganoidVarAnalysis

oshlack.github.io

Oshlack Lab website

paed-cf-cite-seq

TALLSorts

AllSorts_v1

An Acute Lymphoblasitc Leukemia B-Cell classifier

TobleroneApp

Desktop app incorporating https://github.com/oshlack/toblerone

Damsel

ec-dtu-paper

Fast and accurate differential transcript usage by testing equivalence class counts

MINTIE-paper-analysis

Code for generating the figures and analyses presented in the MINTIE paper

pooled-parents-paper

Code and analysis for the pooled parents paper

TopDeck

xenanoseq

Nanopore demultiplexing, QC and alignment pipeline for xenograph RNA-seq experiments