Oshlack/Oncopipe

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Created almost 8 years ago
Updated about 7 years ago

Oshlack/Oncopipe

Oshlack

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Clinical pipeline for detecting gene fusions in RNAseq data utilising JAFFA.

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.

splatter-paper

Data and analysis for the Splatter paper

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.

MethylationAnalysisWorkflow

A cross-package Bioconductor workflow for analysing methylation array data

missMethyl

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

GeneLengthBias-scRNASeq

Analysis scripts for eight different scRNASeq datasets that differ in terms of protocol, species and cell type

superTranscript_paper_code

This repository contains code and scripts used to generate and analyse data for the superTranscript/Lace paper.

Jupyter Notebook

combes-organoid-paper

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

scRNAtools-paper

A review of tools for analysing single-cell RNA-seq data

methyl-geneset-testing

Toblerone

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

paed-cf-cite-seq

OrganoidVarAnalysis

TALLSorts

oshlack.github.io

Oshlack Lab website

ALL-RNAseq-utility-paper