oshlack Goto Github PK

all-rnaseq-utility-paper

allsorts

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

allsorts_v1

An Acute Lymphoblasitc Leukemia B-Cell classifier

clinker

Gene Fusion Visualiser

clustree-paper

Paper describing the clustering tree visualisation

combes-organoid-paper

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

corset

Software for clustering de novo assembled transcripts and counting overlapping reads

damsel

ec-dtu-paper

Fast and accurate differential transcript usage by testing equivalence class counts

ec-dtu-pipe

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

farlie_emu_wing_rnaseq_analysis

This repository contains code from the paper Farlie et al.

genelengthbias-scrnaseq

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

hashtag-demux-paper

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

jaffa

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

lace

Building SuperTranscripts: A linear representation of transcriptome data

methyl-geneset-testing

methylationanalysisworkflow

A cross-package Bioconductor workflow for analysing methylation array data

mintie

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

mintie-paper-analysis

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

missmethyl

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

necklace

Combine reference and assembled transcriptomes for RNA-Seq analysis

oncopipe

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

organoidvaranalysis

oshlack.github.io

Oshlack Lab website

paed-cf-cite-seq

pooled-parents-paper

Code and analysis for the pooled parents paper

scrnatools-paper

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

slinker

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

speckle

R package for specialised analysis of single cell data

splatter

Simple simulation of single-cell RNA sequencing data