Oshlack/splatter-paper

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R
License
MIT License
Created over 7 years ago
Updated almost 7 years ago

Oshlack/splatter-paper

Oshlack

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Data and analysis for the Splatter paper

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.

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

Oncopipe

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