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splatter
Simple simulation of single-cell RNA sequencing dataJAFFA
JAFFA is a multi-step pipeline that takes either raw RNA-Seq reads, or pre-assembled transcripts, then searches for gene fusionsCorset
Software for clustering de novo assembled transcripts and counting overlapping readsLace
Building SuperTranscripts: A linear representation of transcriptome dataSTRetch
Method for detecting STR expansions from short-read sequencing dataClinker
Gene Fusion Visualiserspeckle
R package for specialised analysis of single cell dataMINTIE
Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.splatter-paper
Data and analysis for the Splatter papernecklace
Combine reference and assembled transcriptomes for RNA-Seq analysisSlinker
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 datamissMethyl
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 typesuperTranscript_paper_code
This repository contains code and scripts used to generate and analyse data for the superTranscript/Lace paper.combes-organoid-paper
Analysis code and output for the Combes kidney organoid scRNA-seq paper https://doi.org/10.1186/s13073-019-0615-0scRNAtools-paper
A review of tools for analysing single-cell RNA-seq datamethyl-geneset-testing
Toblerone
ec-dtu-pipe
Pipeline for performing differential transcript usage analysis using equivalence classes, transcript quantifications and/or exon countspaed-cf-cite-seq
OrganoidVarAnalysis
TALLSorts
oshlack.github.io
Oshlack Lab websiteALL-RNAseq-utility-paper
Oncopipe
Clinical pipeline for detecting gene fusions in RNAseq data utilising JAFFA.Love Open Source and this site? Check out how you can help us